[{"citation":{"ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Constrained PRFs for unbounded inputs,” presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA, 2016, vol. 9610, pp. 413–428.","ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Constrained PRFs for unbounded inputs. In: Vol 9610. Springer; 2016:413-428. doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>","short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 413–428.","chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Constrained PRFs for Unbounded Inputs,” 9610:413–28. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>.","ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Constrained PRFs for unbounded inputs. CT-RSA: Topics in Cryptology, LNCS, vol. 9610, 413–428.","apa":"Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Constrained PRFs for unbounded inputs (Vol. 9610, pp. 413–428). Presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>","mla":"Abusalah, Hamza M., et al. <i>Constrained PRFs for Unbounded Inputs</i>. Vol. 9610, Springer, 2016, pp. 413–28, doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>."},"intvolume":"      9610","scopus_import":1,"file_date_updated":"2020-07-14T12:44:41Z","ddc":["005","600"],"oa_version":"Submitted Version","date_published":"2016-02-02T00:00:00Z","doi":"10.1007/978-3-319-29485-8_24","publication_status":"published","conference":{"name":"CT-RSA: Topics in Cryptology","start_date":"2016-02-29","location":"San Francisco, CA, USA","end_date":"2016-03-04"},"month":"02","ec_funded":1,"status":"public","oa":1,"_id":"1236","abstract":[{"lang":"eng","text":"A constrained pseudorandom function F: K × X → Y for a family T ⊆ 2X of subsets of X is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a constrained key kS which allows to evaluate F (k, ·) on all inputs x ∈ S, while even given this key, the outputs on all inputs x ∉ S look random. At Asiacrypt’13 Boneh and Waters gave a construction which supports the most general set family so far. Its keys kc are defined for sets decided by boolean circuits C and enable evaluation of the PRF on any x ∈ X where C(x) = 1. In their construction the PRF input length and the size of the circuits C for which constrained keys can be computed must be fixed beforehand during key generation. We construct a constrained PRF that has an unbounded input length and whose constrained keys can be defined for any set recognized by a Turing machine. The only a priori bound we make is on the description size of the machines. We prove our construction secure assuming publiccoin differing-input obfuscation. As applications of our constrained PRF we build a broadcast encryption scheme where the number of potential receivers need not be fixed at setup (in particular, the length of the keys is independent of the number of parties) and the first identity-based non-interactive key exchange protocol with no bound on the number of parties that can agree on a shared key."}],"date_updated":"2023-09-07T12:30:22Z","year":"2016","quality_controlled":"1","volume":9610,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"83"}]},"pubrep_id":"764","publist_id":"6097","type":"conference","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","page":"413 - 428","date_created":"2018-12-11T11:50:52Z","alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"Constrained PRFs for unbounded inputs","author":[{"full_name":"Abusalah, Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","last_name":"Abusalah","first_name":"Hamza M"},{"full_name":"Fuchsbauer, Georg","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"}],"project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":495176,"file_id":"4664","checksum":"3851cee49933ae13b1272e516f213e13","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:44:41Z","file_name":"IST-2017-764-v1+1_279.pdf","date_created":"2018-12-12T10:08:05Z"}],"acknowledgement":"Supported by the European Research Council, ERC Starting Grant (259668-PSPC).","day":"02"},{"doi":"10.1007/978-3-319-39441-1_13","conference":{"start_date":"2016-06-15","name":"CTIC: Computational Topology in Image Context","end_date":"2016-06-17","location":"Marseille, France"},"publication_status":"published","oa_version":"None","date_published":"2016-06-02T00:00:00Z","scopus_import":1,"citation":{"short":"M. Krcál, P. Pilarczyk, in:, Springer, 2016, pp. 140–151.","ama":"Krcál M, Pilarczyk P. Computation of cubical Steenrod squares. In: Vol 9667. Springer; 2016:140-151. doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">10.1007/978-3-319-39441-1_13</a>","ieee":"M. Krcál and P. Pilarczyk, “Computation of cubical Steenrod squares,” presented at the CTIC: Computational Topology in Image Context, Marseille, France, 2016, vol. 9667, pp. 140–151.","chicago":"Krcál, Marek, and Pawel Pilarczyk. “Computation of Cubical Steenrod Squares,” 9667:140–51. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">https://doi.org/10.1007/978-3-319-39441-1_13</a>.","ista":"Krcál M, Pilarczyk P. 2016. Computation of cubical Steenrod squares. CTIC: Computational Topology in Image Context, LNCS, vol. 9667, 140–151.","mla":"Krcál, Marek, and Pawel Pilarczyk. <i>Computation of Cubical Steenrod Squares</i>. Vol. 9667, Springer, 2016, pp. 140–51, doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">10.1007/978-3-319-39441-1_13</a>.","apa":"Krcál, M., &#38; Pilarczyk, P. (2016). Computation of cubical Steenrod squares (Vol. 9667, pp. 140–151). Presented at the CTIC: Computational Topology in Image Context, Marseille, France: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">https://doi.org/10.1007/978-3-319-39441-1_13</a>"},"intvolume":"      9667","abstract":[{"lang":"eng","text":"Bitmap images of arbitrary dimension may be formally perceived as unions of m-dimensional boxes aligned with respect to a rectangular grid in ℝm. Cohomology and homology groups are well known topological invariants of such sets. Cohomological operations, such as the cup product, provide higher-order algebraic topological invariants, especially important for digital images of dimension higher than 3. If such an operation is determined at the level of simplicial chains [see e.g. González-Díaz, Real, Homology, Homotopy Appl, 2003, 83-93], then it is effectively computable. However, decomposing a cubical complex into a simplicial one deleteriously affects the efficiency of such an approach. In order to avoid this overhead, a direct cubical approach was applied in [Pilarczyk, Real, Adv. Comput. Math., 2015, 253-275] for the cup product in cohomology, and implemented in the ChainCon software package [http://www.pawelpilarczyk.com/chaincon/]. We establish a formula for the Steenrod square operations [see Steenrod, Annals of Mathematics. Second Series, 1947, 290-320] directly at the level of cubical chains, and we prove the correctness of this formula. An implementation of this formula is programmed in C++ within the ChainCon software framework. We provide a few examples and discuss the effectiveness of this approach. One specific application follows from the fact that Steenrod squares yield tests for the topological extension problem: Can a given map A → Sd to a sphere Sd be extended to a given super-complex X of A? In particular, the ROB-SAT problem, which is to decide for a given function f: X → ℝm and a value r &gt; 0 whether every g: X → ℝm with ∥g - f ∥∞ ≤ r has a root, reduces to the extension problem."}],"date_updated":"2021-01-12T06:49:18Z","year":"2016","_id":"1237","status":"public","month":"06","ec_funded":1,"date_created":"2018-12-11T11:50:52Z","page":"140 - 151","type":"conference","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"language":[{"iso":"eng"}],"publist_id":"6096","quality_controlled":"1","volume":9667,"acknowledgement":"The research conducted by both authors has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreements no. 291734 (for M. K.) and no. 622033 (for P. P.).","day":"02","author":[{"full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál","first_name":"Marek"},{"first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel"}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps","_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"Computation of cubical Steenrod squares","alternative_title":["LNCS"]},{"publist_id":"6094","pubrep_id":"710","volume":6,"quality_controlled":"1","date_created":"2018-12-11T11:50:53Z","publication":"Frontiers in Plant Science","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"type":"journal_article","title":"Endosomal interactions during root hair growth","publisher":"Frontiers Research Foundation","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"29","acknowledgement":"This work was supported by National Program for Sustainability I (grant no. LO1204) provided by the Czech Ministry of Education and by Institutional Fund of Palacký University Olomouc (GK and OŠ).\r\nWe thank Sabine Fischer for help with the statistics.","file":[{"file_id":"4760","creator":"system","checksum":"3127eab844d53564bf47e2b6b42f1ca0","access_level":"open_access","file_name":"IST-2016-710-v1+1_fpls-06-01262.pdf","date_updated":"2020-07-14T12:44:41Z","date_created":"2018-12-12T10:09:36Z","relation":"main_file","content_type":"application/pdf","file_size":1640550}],"author":[{"full_name":"Von Wangenheim, Daniel","first_name":"Daniel","orcid":"0000-0002-6862-1247","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rosero, Amparo","first_name":"Amparo","last_name":"Rosero"},{"first_name":"George","last_name":"Komis","full_name":"Komis, George"},{"full_name":"Šamajová, Olga","first_name":"Olga","last_name":"Šamajová"},{"first_name":"Miroslav","last_name":"Ovečka","full_name":"Ovečka, Miroslav"},{"last_name":"Voigt","first_name":"Boris","full_name":"Voigt, Boris"},{"full_name":"Šamaj, Jozef","first_name":"Jozef","last_name":"Šamaj"}],"ddc":["581"],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:41Z","intvolume":"         6","citation":{"chicago":"Wangenheim, Daniel von, Amparo Rosero, George Komis, Olga Šamajová, Miroslav Ovečka, Boris Voigt, and Jozef Šamaj. “Endosomal Interactions during Root Hair Growth.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2016. <a href=\"https://doi.org/10.3389/fpls.2015.01262\">https://doi.org/10.3389/fpls.2015.01262</a>.","mla":"von Wangenheim, Daniel, et al. “Endosomal Interactions during Root Hair Growth.” <i>Frontiers in Plant Science</i>, vol. 6, no. JAN2016, 1262, Frontiers Research Foundation, 2016, doi:<a href=\"https://doi.org/10.3389/fpls.2015.01262\">10.3389/fpls.2015.01262</a>.","ista":"von Wangenheim D, Rosero A, Komis G, Šamajová O, Ovečka M, Voigt B, Šamaj J. 2016. Endosomal interactions during root hair growth. Frontiers in Plant Science. 6(JAN2016), 1262.","apa":"von Wangenheim, D., Rosero, A., Komis, G., Šamajová, O., Ovečka, M., Voigt, B., &#38; Šamaj, J. (2016). Endosomal interactions during root hair growth. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2015.01262\">https://doi.org/10.3389/fpls.2015.01262</a>","short":"D. von Wangenheim, A. Rosero, G. Komis, O. Šamajová, M. Ovečka, B. Voigt, J. Šamaj, Frontiers in Plant Science 6 (2016).","ama":"von Wangenheim D, Rosero A, Komis G, et al. Endosomal interactions during root hair growth. <i>Frontiers in Plant Science</i>. 2016;6(JAN2016). doi:<a href=\"https://doi.org/10.3389/fpls.2015.01262\">10.3389/fpls.2015.01262</a>","ieee":"D. von Wangenheim <i>et al.</i>, “Endosomal interactions during root hair growth,” <i>Frontiers in Plant Science</i>, vol. 6, no. JAN2016. Frontiers Research Foundation, 2016."},"publication_status":"published","doi":"10.3389/fpls.2015.01262","date_published":"2016-01-29T00:00:00Z","oa_version":"Published Version","oa":1,"status":"public","month":"01","year":"2016","date_updated":"2021-01-12T06:49:18Z","abstract":[{"lang":"eng","text":"The dynamic localization of endosomal compartments labeled with targeted fluorescent protein tags is routinely followed by time lapse fluorescence microscopy approaches and single particle tracking algorithms. In this way trajectories of individual endosomes can be mapped and linked to physiological processes as cell growth. However, other aspects of dynamic behavior including endosomal interactions are difficult to follow in this manner. Therefore, we characterized the localization and dynamic properties of early and late endosomes throughout the entire course of root hair formation by means of spinning disc time lapse imaging and post-acquisition automated multitracking and quantitative analysis. Our results show differential motile behavior of early and late endosomes and interactions of late endosomes that may be specified to particular root hair domains. Detailed data analysis revealed a particular transient interaction between late endosomes—termed herein as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially located in the root hair tip interacted as dancing-endosomes and traveled short distances during this interaction. Finally, sizes of early and late endosomes were addressed by means of super-resolution structured illumination microscopy (SIM) to corroborate measurements on the spinning disc. This is a first study providing quantitative microscopic data on dynamic spatio-temporal interactions of endosomes during root hair tip growth."}],"issue":"JAN2016","_id":"1238","article_number":"1262"},{"year":"2016","day":"15","abstract":[{"text":"Nonadherent polarized cells have been observed to have a pearlike, elongated shape. Using a minimal model that describes the cell cortex as a thin layer of contractile active gel, we show that the anisotropy of active stresses, controlled by cortical viscosity and filament ordering, can account for this morphology. The predicted shapes can be determined from the flow pattern only; they prove to be independent of the mechanism at the origin of the cortical flow, and are only weakly sensitive to the cytoplasmic rheology. In the case of actin flows resulting from a contractile instability, we propose a phase diagram of three-dimensional cell shapes that encompasses nonpolarized spherical, elongated, as well as oblate shapes, all of which have been observed in experiment.","lang":"eng"}],"acknowledgement":"V. R. acknowledges support by the Austrian Science Fund (FWF): (Grant No. T560-B17).","issue":"2","date_updated":"2021-01-12T06:49:19Z","_id":"1239","author":[{"first_name":"Andrew","last_name":"Callan Jones","full_name":"Callan Jones, Andrew"},{"first_name":"Verena","orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","full_name":"Ruprecht, Verena"},{"full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217","first_name":"Stefan","last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Raphaël","last_name":"Voituriez","full_name":"Voituriez, Raphaël"}],"article_number":"028102","project":[{"_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","call_identifier":"FWF"}],"title":"Cortical flow-driven shapes of nonadherent cells","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","status":"public","month":"01","publication":"Physical Review Letters","date_created":"2018-12-11T11:50:53Z","doi":"10.1103/PhysRevLett.116.028102","publication_status":"published","date_published":"2016-01-15T00:00:00Z","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","scopus_import":1,"publist_id":"6095","volume":116,"quality_controlled":"1","citation":{"chicago":"Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg, and Raphaël Voituriez. “Cortical Flow-Driven Shapes of Nonadherent Cells.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">https://doi.org/10.1103/PhysRevLett.116.028102</a>.","apa":"Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., &#38; Voituriez, R. (2016). Cortical flow-driven shapes of nonadherent cells. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">https://doi.org/10.1103/PhysRevLett.116.028102</a>","ista":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016. Cortical flow-driven shapes of nonadherent cells. Physical Review Letters. 116(2), 028102.","mla":"Callan Jones, Andrew, et al. “Cortical Flow-Driven Shapes of Nonadherent Cells.” <i>Physical Review Letters</i>, vol. 116, no. 2, 028102, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">10.1103/PhysRevLett.116.028102</a>.","short":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez, Physical Review Letters 116 (2016).","ieee":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez, “Cortical flow-driven shapes of nonadherent cells,” <i>Physical Review Letters</i>, vol. 116, no. 2. American Physical Society, 2016.","ama":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Cortical flow-driven shapes of nonadherent cells. <i>Physical Review Letters</i>. 2016;116(2). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">10.1103/PhysRevLett.116.028102</a>"},"intvolume":"       116"},{"oa":1,"status":"public","month":"01","year":"2016","date_updated":"2021-01-12T06:49:20Z","abstract":[{"lang":"eng","text":"Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. Here, we characterize lncRNA natural expression variability in human primary granulocytes. Results: We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple lncRNAs absent from reference annotations, and use this to investigate three known features (higher tissue-specificity, lower expression, and reduced splicing efficiency) of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals sampled three times at 1- or more than 1-month intervals. We show that lncRNAs display significantly more inter-individual expression variability compared to mRNAs. We confirm this finding in two independent human datasets by analyzing multiple tissues from the GTEx project and lymphoblastoid cell lines from the GEUVADIS project. Using the latter dataset we also show that including more human donors into the transcriptome annotation pipeline allows identification of an increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions: A comprehensive annotation of lncRNAs is known to require an approach that is sensitive to low and tight tissue-specific expression. Here we show that increased inter-individual expression variability is an additional general lncRNA feature to consider when creating a comprehensive annotation of human lncRNAs or proposing their use as prognostic or disease markers."}],"issue":"1","_id":"1240","article_number":"14","ddc":["576"],"file_date_updated":"2020-07-14T12:44:41Z","scopus_import":1,"citation":{"chicago":"Kornienko, Aleksandra, Christoph Dotter, Philipp Guenzl, Heinz Gisslinger, Bettina Gisslinger, Ciara Cleary, Robert Kralovics, Florian Pauler, and Denise Barlow. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” <i>Genome Biology</i>. BioMed Central, 2016. <a href=\"https://doi.org/10.1186/s13059-016-0873-8\">https://doi.org/10.1186/s13059-016-0873-8</a>.","ista":"Kornienko A, Dotter C, Guenzl P, Gisslinger H, Gisslinger B, Cleary C, Kralovics R, Pauler F, Barlow D. 2016. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biology. 17(1), 14.","apa":"Kornienko, A., Dotter, C., Guenzl, P., Gisslinger, H., Gisslinger, B., Cleary, C., … Barlow, D. (2016). Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-016-0873-8\">https://doi.org/10.1186/s13059-016-0873-8</a>","mla":"Kornienko, Aleksandra, et al. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” <i>Genome Biology</i>, vol. 17, no. 1, 14, BioMed Central, 2016, doi:<a href=\"https://doi.org/10.1186/s13059-016-0873-8\">10.1186/s13059-016-0873-8</a>.","ieee":"A. Kornienko <i>et al.</i>, “Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans,” <i>Genome Biology</i>, vol. 17, no. 1. BioMed Central, 2016.","ama":"Kornienko A, Dotter C, Guenzl P, et al. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. <i>Genome Biology</i>. 2016;17(1). doi:<a href=\"https://doi.org/10.1186/s13059-016-0873-8\">10.1186/s13059-016-0873-8</a>","short":"A. Kornienko, C. Dotter, P. Guenzl, H. Gisslinger, B. Gisslinger, C. Cleary, R. Kralovics, F. Pauler, D. Barlow, Genome Biology 17 (2016)."},"intvolume":"        17","publication_status":"published","doi":"10.1186/s13059-016-0873-8","date_published":"2016-01-29T00:00:00Z","oa_version":"Published Version","title":"Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans","publisher":"BioMed Central","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"29","acknowledgement":"This study was partly funded by the Austrian Science Fund (FWF F43-B09, FWF W1207-B09). PMG is a recipient of a DOC Fellowship of the Austrian Academy of Sciences.\r\nWe thank Ruth Klement, Tomasz Kulinski, Elisangela Valente, Elisabeth Salzer,\r\nand Roland Jäger for technical/bioinformatic assistance and advice, the CeMM\r\nIT department and José Manuel Molero for help and advice on software usage,\r\nthe Biomedical Sequencing Facility (http://biomedical-sequencing.at/) for\r\nsequencing and advice, Jacques Colinge, Daniel Andergassen, and Tomasz\r\nKulinski for discussions, Quanah Hudson and Jörg Menche for reading and\r\ncommenting on the manuscript.","file":[{"file_size":2914601,"content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:10:05Z","date_updated":"2020-07-14T12:44:41Z","file_name":"IST-2016-709-v1+1_s13059-016-0873-8.pdf","access_level":"open_access","file_id":"4789","checksum":"a268beee1a690801c83ec6729f9ebc5b","creator":"system"}],"author":[{"full_name":"Kornienko, Aleksandra","first_name":"Aleksandra","last_name":"Kornienko"},{"first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","full_name":"Dotter, Christoph"},{"last_name":"Guenzl","first_name":"Philipp","full_name":"Guenzl, Philipp"},{"full_name":"Gisslinger, Heinz","last_name":"Gisslinger","first_name":"Heinz"},{"full_name":"Gisslinger, Bettina","first_name":"Bettina","last_name":"Gisslinger"},{"full_name":"Cleary, Ciara","last_name":"Cleary","first_name":"Ciara"},{"full_name":"Kralovics, Robert","last_name":"Kralovics","first_name":"Robert"},{"full_name":"Pauler, Florian","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"full_name":"Barlow, Denise","last_name":"Barlow","first_name":"Denise"}],"publist_id":"6093","pubrep_id":"709","quality_controlled":"1","volume":17,"date_created":"2018-12-11T11:50:53Z","publication":"Genome Biology","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"type":"journal_article"},{"quality_controlled":"1","volume":202,"publist_id":"6091","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"type":"journal_article","date_created":"2018-12-11T11:50:54Z","page":"721 - 732","publication":"Genetics","title":"The role of recombination in evolutionary rescue","publisher":"Genetics Society of America","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"L'OREAL Fellowship"}],"author":[{"last_name":"Uecker","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","first_name":"Hildegard","full_name":"Uecker, Hildegard"},{"full_name":"Hermisson, Joachim","last_name":"Hermisson","first_name":"Joachim"}],"day":"01","acknowledgement":"This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton).","intvolume":"       202","citation":{"short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. <i>Genetics</i>. 2016;202(2):721-732. doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>","ieee":"H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.","chicago":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>.","mla":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>.","apa":"Uecker, H., &#38; Hermisson, J. (2016). The role of recombination in evolutionary rescue. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732."},"main_file_link":[{"url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract","open_access":"1"}],"scopus_import":1,"date_published":"2016-02-01T00:00:00Z","oa_version":"Preprint","publication_status":"published","doi":"10.1534/genetics.115.180299","ec_funded":1,"month":"02","oa":1,"status":"public","_id":"1241","year":"2016","date_updated":"2023-02-21T10:24:19Z","issue":"2","abstract":[{"text":"How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances.","lang":"eng"}]},{"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"date_created":"2018-12-11T11:50:54Z","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","volume":93,"quality_controlled":"1","publist_id":"6088","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Sokolowski","id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R"},{"full_name":"Walczak, Aleksandra","last_name":"Walczak","first_name":"Aleksandra"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper"}],"acknowledgement":"We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions. This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370 from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W. acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561. G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S.","day":"04","publisher":"American Institute of Physics","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Extending the dynamic range of transcription factor action by translational regulation","oa_version":"Preprint","date_published":"2016-02-04T00:00:00Z","publication_status":"published","doi":"10.1103/PhysRevE.93.022404","intvolume":"        93","citation":{"ieee":"T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2. American Institute of Physics, 2016.","ama":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2016;93(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>","short":"T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).","apa":"Sokolowski, T. R., Walczak, A., Bialek, W., &#38; Tkačik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>","ista":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.","mla":"Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>.","chicago":"Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>."},"scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1507.02562","open_access":"1"}],"article_number":"022404","_id":"1242","date_updated":"2021-01-12T06:49:20Z","abstract":[{"lang":"eng","text":"A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression."}],"issue":"2","year":"2016","month":"02","status":"public","oa":1},{"project":[{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","orcid":"0000-0001-7460-7479","first_name":"Maros","full_name":"Pleska, Maros"},{"full_name":"Qian, Long","last_name":"Qian","first_name":"Long"},{"full_name":"Okura, Reiko","last_name":"Okura","first_name":"Reiko"},{"last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"last_name":"Wakamoto","first_name":"Yuichi","full_name":"Wakamoto, Yuichi"},{"full_name":"Kussell, Edo","first_name":"Edo","last_name":"Kussell"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C"}],"day":"08","acknowledgement":"This work was funded by an HFSP Young Investigators’ grant. M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria. R.O. and Y.W. were supported by the Platform for Dynamic Approaches to Living System from MEXT, Japan. We wish to thank I. Kobayashi for providing us with the EcoRI and EcoRV plasmids, and A. Campbell for providing us with the λ vir phage. We thank D. Siekhaus and C. Uhler and members of the C.C.G. and J.P. Bollback laboratories for in-depth discussions. We thank B. Stern for comments on an earlier version of the manuscript. We especially thank B.R. Levin for advice and comments, and the anonymous reviewers for significantly improving the manuscript.","title":"Bacterial autoimmunity due to a restriction-modification system","publisher":"Cell Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"type":"journal_article","page":"404 - 409","date_created":"2018-12-11T11:50:54Z","publication":"Current Biology","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"202"}]},"quality_controlled":"1","volume":26,"publist_id":"6087","_id":"1243","year":"2016","date_updated":"2023-09-07T11:59:32Z","abstract":[{"text":"Restriction-modification (RM) systems represent a minimal and ubiquitous biological system of self/non-self discrimination in prokaryotes [1], which protects hosts from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase (M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by methylating short specific DNA sequences called restriction sites, whereas R recognizes unmethylated restriction sites as non-self and introduces a double-stranded DNA break [3]. Restriction sites are significantly underrepresented in prokaryotic genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore, RM systems can promote DNA recombination [9] and contribute to genetic variation in microbial populations, thus facilitating adaptive evolution [10]. However, cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has not been directly detected, and its cause, frequency, and outcome are unknown. We quantify self-restriction caused by two RM systems of Escherichia coli and find that, in agreement with levels of restriction site avoidance, EcoRI, but not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic process, which temporarily induces the SOS response, and is followed by DNA repair, maintaining cell viability. We find that RM systems with higher restriction efficiency against bacteriophage infections exhibit a higher rate of self-restriction, and that this rate can be further increased by stochastic imbalance between R and M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic genomes.","lang":"eng"}],"issue":"3","month":"02","status":"public","date_published":"2016-02-08T00:00:00Z","oa_version":"None","publication_status":"published","doi":"10.1016/j.cub.2015.12.041","intvolume":"        26","citation":{"short":"M. Pleska, L. Qian, R. Okura, T. Bergmiller, Y. Wakamoto, E. Kussell, C.C. Guet, Current Biology 26 (2016) 404–409.","ama":"Pleska M, Qian L, Okura R, et al. Bacterial autoimmunity due to a restriction-modification system. <i>Current Biology</i>. 2016;26(3):404-409. doi:<a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">10.1016/j.cub.2015.12.041</a>","ieee":"M. Pleska <i>et al.</i>, “Bacterial autoimmunity due to a restriction-modification system,” <i>Current Biology</i>, vol. 26, no. 3. Cell Press, pp. 404–409, 2016.","apa":"Pleska, M., Qian, L., Okura, R., Bergmiller, T., Wakamoto, Y., Kussell, E., &#38; Guet, C. C. (2016). Bacterial autoimmunity due to a restriction-modification system. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">https://doi.org/10.1016/j.cub.2015.12.041</a>","ista":"Pleska M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, Guet CC. 2016. Bacterial autoimmunity due to a restriction-modification system. Current Biology. 26(3), 404–409.","mla":"Pleska, Maros, et al. “Bacterial Autoimmunity Due to a Restriction-Modification System.” <i>Current Biology</i>, vol. 26, no. 3, Cell Press, 2016, pp. 404–09, doi:<a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">10.1016/j.cub.2015.12.041</a>.","chicago":"Pleska, Maros, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto, Edo Kussell, and Calin C Guet. “Bacterial Autoimmunity Due to a Restriction-Modification System.” <i>Current Biology</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">https://doi.org/10.1016/j.cub.2015.12.041</a>."},"scopus_import":1},{"status":"public","oa":1,"month":"02","issue":"7","abstract":[{"text":"Cell polarity refers to a functional spatial organization of proteins that is crucial for the control of essential cellular processes such as growth and division. To establish polarity, cells rely on elaborate regulation networks that control the distribution of proteins at the cell membrane. In fission yeast cells, a microtubule-dependent network has been identified that polarizes the distribution of signaling proteins that restricts growth to cell ends and targets the cytokinetic machinery to the middle of the cell. Although many molecular components have been shown to play a role in this network, it remains unknown which molecular functionalities are minimally required to establish a polarized protein distribution in this system. Here we show that a membrane-binding protein fragment, which distributes homogeneously in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching it to a cytoplasmic microtubule end-binding protein. This concentration results in a polarized pattern of chimera proteins with a spatial extension that is very reminiscent of natural polarity patterns in fission yeast. However, chimera levels fluctuate in response to microtubule dynamics, and disruption of microtubules leads to disappearance of the pattern. Numerical simulations confirm that the combined functionality of membrane anchoring and microtubule tip affinity is in principle sufficient to create polarized patterns. Our chimera protein may thus represent a simple molecular functionality that is able to polarize the membrane, onto which additional layers of molecular complexity may be built to provide the temporal robustness that is typical of natural polarity patterns.","lang":"eng"}],"date_updated":"2021-01-12T06:49:21Z","year":"2016","_id":"1244","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/","open_access":"1"}],"scopus_import":1,"intvolume":"       113","citation":{"chicago":"Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1419248113\">https://doi.org/10.1073/pnas.1419248113</a>.","apa":"Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., &#38; Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1419248113\">https://doi.org/10.1073/pnas.1419248113</a>","ista":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.","mla":"Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>, vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:<a href=\"https://doi.org/10.1073/pnas.1419248113\">10.1073/pnas.1419248113</a>.","short":"P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816.","ieee":"P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom, “Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells,” <i>PNAS</i>, vol. 113, no. 7. National Academy of Sciences, pp. 1811–1816, 2016.","ama":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. <i>PNAS</i>. 2016;113(7):1811-1816. doi:<a href=\"https://doi.org/10.1073/pnas.1419248113\">10.1073/pnas.1419248113</a>"},"doi":"10.1073/pnas.1419248113","publication_status":"published","oa_version":"Submitted Version","date_published":"2016-02-16T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","title":"Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells","acknowledgement":"We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions; and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”","day":"16","author":[{"full_name":"Recouvreux, Pierre","last_name":"Recouvreux","first_name":"Pierre"},{"last_name":"Sokolowski","id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","first_name":"Thomas R","full_name":"Sokolowski, Thomas R"},{"first_name":"Aristea","last_name":"Grammoustianou","full_name":"Grammoustianou, Aristea"},{"last_name":"Tenwolde","first_name":"Pieter","full_name":"Tenwolde, Pieter"},{"last_name":"Dogterom","first_name":"Marileen","full_name":"Dogterom, Marileen"}],"publist_id":"6085","volume":113,"quality_controlled":"1","publication":"PNAS","date_created":"2018-12-11T11:50:55Z","page":"1811 - 1816","type":"journal_article","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"To facilitate collaboration in massive online classrooms, instructors must make many decisions. For instance, the following parameters need to be decided when designing a peer-feedback system where students review each others' essays: the number of students each student must provide feedback to, an algorithm to map feedback providers to receivers, constraints that ensure students do not become free-riders (receiving feedback but not providing it), the best times to receive feedback to improve learning etc. While instructors can answer these questions by running experiments or invoking past experience, game-theoretic models with data from online learning platforms can identify better initial designs for further improvements. As an example, we explore the design space of a peer feedback system by modeling it using game theory. Our simulations show that incentivizing students to provide feedback requires the value obtained from receiving a feedback to exceed the cost of providing it by a large factor (greater than 7). Furthermore, hiding feedback from low-effort students incentivizes them to provide more feedback."}],"issue":"Februar-2016","date_updated":"2021-01-12T06:49:22Z","year":"2016","_id":"1245","status":"public","month":"02","ec_funded":1,"doi":"10.1145/2818052.2869122","publication_status":"published","conference":{"start_date":"2016-02-26","name":"CSCW: Computer Supported Cooperative Work and Social Computing","end_date":"2016-03-02","location":"San Francisco, CA, USA"},"oa_version":"None","date_published":"2016-02-27T00:00:00Z","scopus_import":1,"intvolume":"        26","citation":{"short":"V. Pandey, K. Chatterjee, in:, Proceedings of the ACM Conference on Computer Supported Cooperative Work, ACM, 2016, pp. 365–368.","ama":"Pandey V, Chatterjee K. Game-theoretic models identify useful principles for peer collaboration in online learning platforms. In: <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>. Vol 26. ACM; 2016:365-368. doi:<a href=\"https://doi.org/10.1145/2818052.2869122\">10.1145/2818052.2869122</a>","ieee":"V. Pandey and K. Chatterjee, “Game-theoretic models identify useful principles for peer collaboration in online learning platforms,” in <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>, San Francisco, CA, USA, 2016, vol. 26, no. Februar-2016, pp. 365–368.","chicago":"Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify Useful Principles for Peer Collaboration in Online Learning Platforms.” In <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>, 26:365–68. ACM, 2016. <a href=\"https://doi.org/10.1145/2818052.2869122\">https://doi.org/10.1145/2818052.2869122</a>.","apa":"Pandey, V., &#38; Chatterjee, K. (2016). Game-theoretic models identify useful principles for peer collaboration in online learning platforms. In <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i> (Vol. 26, pp. 365–368). San Francisco, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2818052.2869122\">https://doi.org/10.1145/2818052.2869122</a>","mla":"Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify Useful Principles for Peer Collaboration in Online Learning Platforms.” <i>Proceedings of the ACM Conference on Computer Supported Cooperative Work</i>, vol. 26, no. Februar-2016, ACM, 2016, pp. 365–68, doi:<a href=\"https://doi.org/10.1145/2818052.2869122\">10.1145/2818052.2869122</a>.","ista":"Pandey V, Chatterjee K. 2016. Game-theoretic models identify useful principles for peer collaboration in online learning platforms. Proceedings of the ACM Conference on Computer Supported Cooperative Work. CSCW: Computer Supported Cooperative Work and Social Computing vol. 26, 365–368."},"acknowledgement":"ERC Start Grant Graph Games 279307 supported this  research. ","day":"27","author":[{"full_name":"Pandey, Vineet","first_name":"Vineet","last_name":"Pandey"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"}],"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","title":"Game-theoretic models identify useful principles for peer collaboration in online learning platforms","publication":"Proceedings of the ACM Conference on Computer Supported Cooperative Work","page":"365 - 368","date_created":"2018-12-11T11:50:55Z","type":"conference","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"publist_id":"6083","quality_controlled":"1","volume":26},{"_id":"1246","article_number":"22665","year":"2016","date_updated":"2021-01-12T06:49:22Z","abstract":[{"text":"Near-field imaging is a powerful tool to investigate the complex structure of light at the nanoscale. Recent advances in near-field imaging have indicated the possibility for the complete reconstruction of both electric and magnetic components of the evanescent field. Here we study the electro-magnetic field structure of surface plasmon polariton waves propagating along subwavelength gold nanowires by performing phase- and polarization-resolved near-field microscopy in collection mode. By applying the optical reciprocity theorem, we describe the signal collected by the probe as an overlap integral of the nanowire's evanescent field and the probe's response function. As a result, we find that the probe's sensitivity to the magnetic field is approximately equal to its sensitivity to the electric field. Through rigorous modeling of the nanowire mode as well as the aperture probe response function, we obtain a good agreement between experimentally measured signals and a numerical model. Our findings provide a better understanding of aperture-based near-field imaging of the nanoscopic plasmonic and photonic structures and are helpful for the interpretation of future near-field experiments.","lang":"eng"}],"month":"03","oa":1,"status":"public","date_published":"2016-03-07T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1038/srep22665","intvolume":"         6","citation":{"chicago":"Kabakova, Irina, Anouk De Hoogh, Ruben Van Der Wel, Matthias Wulf, Boris Le Feber, and Laurens Kuipers. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep22665\">https://doi.org/10.1038/srep22665</a>.","mla":"Kabakova, Irina, et al. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” <i>Scientific Reports</i>, vol. 6, 22665, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep22665\">10.1038/srep22665</a>.","ista":"Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. 2016. Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. 6, 22665.","apa":"Kabakova, I., De Hoogh, A., Van Der Wel, R., Wulf, M., Le Feber, B., &#38; Kuipers, L. (2016). Imaging of electric and magnetic fields near plasmonic nanowires. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep22665\">https://doi.org/10.1038/srep22665</a>","ama":"Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. Imaging of electric and magnetic fields near plasmonic nanowires. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep22665\">10.1038/srep22665</a>","ieee":"I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, and L. Kuipers, “Imaging of electric and magnetic fields near plasmonic nanowires,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","short":"I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, L. Kuipers, Scientific Reports 6 (2016)."},"ddc":["539"],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:41Z","file":[{"relation":"main_file","content_type":"application/pdf","file_size":1425165,"checksum":"ca76236cb1aae22cb90c65313e2c5e98","file_id":"5061","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:44:41Z","file_name":"IST-2016-707-v1+1_srep22665.pdf","date_created":"2018-12-12T10:14:11Z"}],"author":[{"full_name":"Kabakova, Irina","first_name":"Irina","last_name":"Kabakova"},{"full_name":"De Hoogh, Anouk","first_name":"Anouk","last_name":"De Hoogh"},{"first_name":"Ruben","last_name":"Van Der Wel","full_name":"Van Der Wel, Ruben"},{"full_name":"Wulf, Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","orcid":"0000-0001-6613-1378"},{"first_name":"Boris","last_name":"Le Feber","full_name":"Le Feber, Boris"},{"full_name":"Kuipers, Laurens","last_name":"Kuipers","first_name":"Laurens"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"07","acknowledgement":"This work is supported part of the research program of the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO), and part of this work has been funded by the project ‘SPANGL4Q’, which acknowledges the financial support of the Future and Emerging Technologies (FET) program within the Seventh Framework Programme for Research of the European Commission, under FETOpen grant number: FP7-284743. L.K. acknowledges funding from ERC Advanced, Investigator Grant (no. 240438-CONSTANS).","title":"Imaging of electric and magnetic fields near plasmonic nanowires","publisher":"Nature Publishing Group","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"type":"journal_article","date_created":"2018-12-11T11:50:55Z","publication":"Scientific Reports","has_accepted_license":"1","quality_controlled":"1","volume":6,"publist_id":"6082","pubrep_id":"707"},{"scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/","open_access":"1"}],"citation":{"short":"M. Karampelias, P. Neyt, S. De Groeve, S. Aesaert, G. Coussens, J. Rolčík, L. Bruno, N. De Winne, A. Van Minnebruggen, M. Van Montagu, M. Ponce, J. Micol, J. Friml, G. De Jaeger, M. Van Lijsebettens, PNAS 113 (2016) 2768–2773.","ama":"Karampelias M, Neyt P, De Groeve S, et al. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. <i>PNAS</i>. 2016;113(10):2768-2773. doi:<a href=\"https://doi.org/10.1073/pnas.1501343112\">10.1073/pnas.1501343112</a>","ieee":"M. Karampelias <i>et al.</i>, “ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling,” <i>PNAS</i>, vol. 113, no. 10. National Academy of Sciences, pp. 2768–2773, 2016.","chicago":"Karampelias, Michael, Pia Neyt, Steven De Groeve, Stijn Aesaert, Griet Coussens, Jakub Rolčík, Leonardo Bruno, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1501343112\">https://doi.org/10.1073/pnas.1501343112</a>.","mla":"Karampelias, Michael, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” <i>PNAS</i>, vol. 113, no. 10, National Academy of Sciences, 2016, pp. 2768–73, doi:<a href=\"https://doi.org/10.1073/pnas.1501343112\">10.1073/pnas.1501343112</a>.","apa":"Karampelias, M., Neyt, P., De Groeve, S., Aesaert, S., Coussens, G., Rolčík, J., … Van Lijsebettens, M. (2016). ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1501343112\">https://doi.org/10.1073/pnas.1501343112</a>","ista":"Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce M, Micol J, Friml J, De Jaeger G, Van Lijsebettens M. 2016. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 113(10), 2768–2773."},"intvolume":"       113","doi":"10.1073/pnas.1501343112","publication_status":"published","oa_version":"Submitted Version","date_published":"2016-03-08T00:00:00Z","status":"public","oa":1,"month":"03","ec_funded":1,"abstract":[{"text":"The shaping of organs in plants depends on the intercellular flow of the phytohormone auxin, of which the directional signaling is determined by the polar subcellular localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID kinase, which act antagonistically to mediate their apical-basal polar delivery. Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant phenotypes [i.e., reduced apical dominance, primary root length, lateral root emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia; decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems; hypergravitropic root growth and response; increased IAA levels in shoot apices; and reduced auxin accumulation in root meristems] support a role for RON3 in auxin biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3 might act in PIN transporter trafficking. Indeed, pharmacological interference with vesicle trafficking processes revealed that single ron3-2 and double ron3-2 rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our data indicate that RON3 contributes to auxin-mediated development by playing a role in PIN recycling and polarity establishment through regulation of the PP2A complex activity.","lang":"eng"}],"issue":"10","date_updated":"2021-01-12T06:49:22Z","year":"2016","_id":"1247","publist_id":"6081","volume":113,"quality_controlled":"1","publication":"PNAS","date_created":"2018-12-11T11:50:56Z","page":"2768 - 2773","type":"journal_article","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","title":"ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling","acknowledgement":"This work was supported by the Ghent University Special Research Fund (M.K.), the European Research Council (Project ERC-2011-StG-20101109-PSDP) (to J.F.), and the Körber European Science Foun-\r\ndation (J.F.). S.D.G. is indebted to the Agency for Science and Technology for\r\na predoctoral fellowship.","day":"08","author":[{"last_name":"Karampelias","first_name":"Michael","full_name":"Karampelias, Michael"},{"first_name":"Pia","last_name":"Neyt","full_name":"Neyt, Pia"},{"last_name":"De Groeve","first_name":"Steven","full_name":"De Groeve, Steven"},{"last_name":"Aesaert","first_name":"Stijn","full_name":"Aesaert, Stijn"},{"full_name":"Coussens, Griet","first_name":"Griet","last_name":"Coussens"},{"full_name":"Rolčík, Jakub","last_name":"Rolčík","first_name":"Jakub"},{"full_name":"Bruno, Leonardo","last_name":"Bruno","first_name":"Leonardo"},{"full_name":"De Winne, Nancy","first_name":"Nancy","last_name":"De Winne"},{"first_name":"Annemie","last_name":"Van Minnebruggen","full_name":"Van Minnebruggen, Annemie"},{"last_name":"Van Montagu","first_name":"Marc","full_name":"Van Montagu, Marc"},{"last_name":"Ponce","first_name":"Maria","full_name":"Ponce, Maria"},{"full_name":"Micol, José","first_name":"José","last_name":"Micol"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"first_name":"Mieke","last_name":"Van Lijsebettens","full_name":"Van Lijsebettens, Mieke"}],"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}]},{"title":"Information processing in living systems","publisher":"Annual Reviews","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"10","acknowledgement":"Our work was supported in part by the US\r\nNational Science Foundation (PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651), by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations.","project":[{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF"}],"author":[{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper"},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William"}],"publist_id":"6080","volume":7,"quality_controlled":"1","date_created":"2018-12-11T11:50:56Z","page":"89 - 117","publication":"Annual Review of Condensed Matter Physics","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"type":"journal_article","oa":1,"status":"public","month":"03","year":"2016","date_updated":"2021-01-12T06:49:23Z","abstract":[{"text":"Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information-theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales.","lang":"eng"}],"_id":"1248","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.8752"}],"scopus_import":1,"intvolume":"         7","citation":{"chicago":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews, 2016. <a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>.","ista":"Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117.","apa":"Tkačik, G., &#38; Bialek, W. (2016). Information processing in living systems. <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>","mla":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” <i>Annual Review of Condensed Matter Physics</i>, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:<a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">10.1146/annurev-conmatphys-031214-014803</a>.","ieee":"G. Tkačik and W. Bialek, “Information processing in living systems,” <i>Annual Review of Condensed Matter Physics</i>, vol. 7. Annual Reviews, pp. 89–117, 2016.","ama":"Tkačik G, Bialek W. Information processing in living systems. <i>Annual Review of Condensed Matter Physics</i>. 2016;7:89-117. doi:<a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">10.1146/annurev-conmatphys-031214-014803</a>","short":"G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117."},"publication_status":"published","doi":"10.1146/annurev-conmatphys-031214-014803","date_published":"2016-03-10T00:00:00Z","oa_version":"Preprint"},{"doi":"10.1016/j.bpj.2016.02.013","publication_status":"published","date_published":"2016-03-29T00:00:00Z","oa_version":"Published Version","ddc":["572","576"],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:41Z","intvolume":"       110","citation":{"ista":"Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. 2016. Determining physical properties of the cell cortex. Biophysical Journal. 110(6), 1421–1429.","apa":"Saha, A., Nishikawa, M., Behrndt, M., Heisenberg, C.-P. J., Julicher, F., &#38; Grill, S. (2016). Determining physical properties of the cell cortex. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">https://doi.org/10.1016/j.bpj.2016.02.013</a>","mla":"Saha, Arnab, et al. “Determining Physical Properties of the Cell Cortex.” <i>Biophysical Journal</i>, vol. 110, no. 6, Biophysical Society, 2016, pp. 1421–29, doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">10.1016/j.bpj.2016.02.013</a>.","chicago":"Saha, Arnab, Masatoshi Nishikawa, Martin Behrndt, Carl-Philipp J Heisenberg, Frank Julicher, and Stephan Grill. “Determining Physical Properties of the Cell Cortex.” <i>Biophysical Journal</i>. Biophysical Society, 2016. <a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">https://doi.org/10.1016/j.bpj.2016.02.013</a>.","short":"A. Saha, M. Nishikawa, M. Behrndt, C.-P.J. Heisenberg, F. Julicher, S. Grill, Biophysical Journal 110 (2016) 1421–1429.","ama":"Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. Determining physical properties of the cell cortex. <i>Biophysical Journal</i>. 2016;110(6):1421-1429. doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.02.013\">10.1016/j.bpj.2016.02.013</a>","ieee":"A. Saha, M. Nishikawa, M. Behrndt, C.-P. J. Heisenberg, F. Julicher, and S. Grill, “Determining physical properties of the cell cortex,” <i>Biophysical Journal</i>, vol. 110, no. 6. Biophysical Society, pp. 1421–1429, 2016."},"year":"2016","issue":"6","abstract":[{"text":"Actin and myosin assemble into a thin layer of a highly dynamic network underneath the membrane of eukaryotic cells. This network generates the forces that drive cell- and tissue-scale morphogenetic processes. The effective material properties of this active network determine large-scale deformations and other morphogenetic events. For example, the characteristic time of stress relaxation (the Maxwell time τM) in the actomyosin sets the timescale of large-scale deformation of the cortex. Similarly, the characteristic length of stress propagation (the hydrodynamic length λ) sets the length scale of slow deformations, and a large hydrodynamic length is a prerequisite for long-ranged cortical flows. Here we introduce a method to determine physical parameters of the actomyosin cortical layer in vivo directly from laser ablation experiments. For this we investigate the cortical response to laser ablation in the one-cell-stage Caenorhabditis elegans embryo and in the gastrulating zebrafish embryo. These responses can be interpreted using a coarse-grained physical description of the cortex in terms of a two-dimensional thin film of an active viscoelastic gel. To determine the Maxwell time τM, the hydrodynamic length λ, the ratio of active stress ζΔμ, and per-area friction γ, we evaluated the response to laser ablation in two different ways: by quantifying flow and density fields as a function of space and time, and by determining the time evolution of the shape of the ablated region. Importantly, both methods provide best-fit physical parameters that are in close agreement with each other and that are similar to previous estimates in the two systems. Our method provides an accurate and robust means for measuring physical parameters of the actomyosin cortical layer. It can be useful for investigations of actomyosin mechanics at the cellular-scale, but also for providing insights into the active mechanics processes that govern tissue-scale morphogenesis.","lang":"eng"}],"date_updated":"2021-01-12T06:49:23Z","_id":"1249","oa":1,"status":"public","month":"03","publication":"Biophysical Journal","page":"1421 - 1429","date_created":"2018-12-11T11:50:56Z","has_accepted_license":"1","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"type":"journal_article","pubrep_id":"706","publist_id":"6079","quality_controlled":"1","volume":110,"day":"29","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"acknowledgement":"S.W.G. acknowledges support by grant no. 281903 from the European Research Council and by grant No. GR-7271/2-1 from the Deutsche Forschungsgemeinschaft. S.W.G. and C.-P.H. acknowledge support through a grant from the Fonds zur Förderung der Wissenschaftlichen Forschung and the Deutsche Forschungsgemeinschaft (No. I930-B20). We are grateful to Daniel Dickinson for providing the LP133 C. elegans strain. We thank G. Salbreux, V. K. Krishnamurthy, and J. S. Bois for fruitful discussions.","file":[{"relation":"main_file","content_type":"application/pdf","file_size":1965645,"file_name":"IST-2016-706-v1+1_1-s2.0-S0006349516001582-main.pdf","date_updated":"2020-07-14T12:44:41Z","date_created":"2018-12-12T10:10:54Z","creator":"system","file_id":"4845","checksum":"c408cf2e25a25c8d711cffea524bda55","access_level":"open_access"}],"author":[{"full_name":"Saha, Arnab","last_name":"Saha","first_name":"Arnab"},{"first_name":"Masatoshi","last_name":"Nishikawa","full_name":"Nishikawa, Masatoshi"},{"first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","full_name":"Behrndt, Martin"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"full_name":"Julicher, Frank","last_name":"Julicher","first_name":"Frank"},{"first_name":"Stephan","last_name":"Grill","full_name":"Grill, Stephan"}],"project":[{"call_identifier":"FWF","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","grant_number":"I 930-B20"}],"title":"Determining physical properties of the cell cortex","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Biophysical Society"},{"title":"Genetic manipulation of glycogen allocation affects replicative lifespan in E coli","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","file":[{"checksum":"53d22b2b39e5adc243d34f18b2615a85","creator":"system","file_id":"5067","access_level":"open_access","file_name":"IST-2016-705-v1+1_journal.pgen.1005974.PDF","date_updated":"2020-07-14T12:44:41Z","date_created":"2018-12-12T10:14:17Z","content_type":"application/pdf","relation":"main_file","file_size":6273249}],"author":[{"first_name":"Alex","last_name":"Boehm","full_name":"Boehm, Alex"},{"last_name":"Arnoldini","first_name":"Markus","full_name":"Arnoldini, Markus"},{"first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","full_name":"Bergmiller, Tobias"},{"last_name":"Röösli","first_name":"Thomas","full_name":"Röösli, Thomas"},{"first_name":"Colette","last_name":"Bigosch","full_name":"Bigosch, Colette"},{"last_name":"Ackermann","first_name":"Martin","full_name":"Ackermann, Martin"}],"day":"19","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"This manuscript is dedicated to the memory of Alex Böhm, who was a great friend and a passionate biologist. Alex passed away after the initial submission of this manuscript. We thank Vesna Olivera and Ursula Sauder from the Zentrum für Mikroskopie Uni Basel for excellent service, and Olin Silander, Nikki Freed, and Nela Nikolic for helpful discussions. This work was supported by the Swiss National Science Foundation grants to M. Ackermann and Urs Jenal (supporting AB).","related_material":{"record":[{"id":"9873","relation":"research_data","status":"public"}]},"volume":12,"quality_controlled":"1","pubrep_id":"705","publist_id":"6077","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"PLoS Genetics","date_created":"2018-12-11T11:50:56Z","has_accepted_license":"1","month":"04","oa":1,"status":"public","_id":"1250","article_number":"e1005974","year":"2016","abstract":[{"text":"In bacteria, replicative aging manifests as a difference in growth or survival between the two cells emerging from division. One cell can be regarded as an aging mother with a decreased potential for future survival and division, the other as a rejuvenated daughter. Here, we aimed at investigating some of the processes involved in aging in the bacterium Escherichia coli, where the two types of cells can be distinguished by the age of their cell poles. We found that certain changes in the regulation of the carbohydrate metabolism can affect aging. A mutation in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative lifespan; csrA mutants stop dividing once their pole exceeds an age of about five divisions. These old-pole cells accumulate glycogen at their old cell poles; after their last division, they do not contain a chromosome, presumably because of spatial exclusion by the glycogen aggregates. The new-pole daughters produced by these aging mothers are born young; they only express the deleterious phenotype once their pole is old. These results demonstrate how manipulations of nutrient allocation can lead to the exclusion of the chromosome and limit replicative lifespan in E. coli, and illustrate how mutations can have phenotypic effects that are specific for cells with old poles. This raises the question how bacteria can avoid the accumulation of such mutations in their genomes over evolutionary times, and how they can achieve the long replicative lifespans that have recently been reported.","lang":"eng"}],"issue":"4","date_updated":"2023-02-23T14:11:39Z","citation":{"short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, PLoS Genetics 12 (2016).","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. <i>PLoS Genetics</i>. 2016;12(4). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974\">10.1371/journal.pgen.1005974</a>","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Genetic manipulation of glycogen allocation affects replicative lifespan in E coli,” <i>PLoS Genetics</i>, vol. 12, no. 4. Public Library of Science, 2016.","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” <i>PLoS Genetics</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pgen.1005974\">https://doi.org/10.1371/journal.pgen.1005974</a>.","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., &#38; Ackermann, M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005974\">https://doi.org/10.1371/journal.pgen.1005974</a>","ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 12(4), e1005974.","mla":"Boehm, Alex, et al. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” <i>PLoS Genetics</i>, vol. 12, no. 4, e1005974, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974\">10.1371/journal.pgen.1005974</a>."},"intvolume":"        12","ddc":["576","579"],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:41Z","date_published":"2016-04-19T00:00:00Z","oa_version":"Published Version","doi":"10.1371/journal.pgen.1005974","publication_status":"published"},{"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863381/"}],"intvolume":"        28","citation":{"chicago":"Zhu, Jinsheng, Aurélien Bailly, Marta Zwiewka, Valpuri Sovero, Martin Di Donato, Pei Ge, Jacqueline Oehri, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” <i>Plant Cell</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1105/tpc.15.00726\">https://doi.org/10.1105/tpc.15.00726</a>.","mla":"Zhu, Jinsheng, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” <i>Plant Cell</i>, vol. 28, no. 4, American Society of Plant Biologists, 2016, pp. 930–48, doi:<a href=\"https://doi.org/10.1105/tpc.15.00726\">10.1105/tpc.15.00726</a>.","ista":"Zhu J, Bailly A, Zwiewka M, Sovero V, Di Donato M, Ge P, Oehri J, Aryal B, Hao P, Linnert M, Burgardt N, Lücke C, Weiwad M, Michel M, Weiergräber O, Pollmann S, Azzarello E, Mancuso S, Ferro N, Fukao Y, Hoffmann C, Wedlich Söldner R, Friml J, Thomas C, Geisler M. 2016. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 28(4), 930–948.","apa":"Zhu, J., Bailly, A., Zwiewka, M., Sovero, V., Di Donato, M., Ge, P., … Geisler, M. (2016). TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.15.00726\">https://doi.org/10.1105/tpc.15.00726</a>","ieee":"J. Zhu <i>et al.</i>, “TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics,” <i>Plant Cell</i>, vol. 28, no. 4. American Society of Plant Biologists, pp. 930–948, 2016.","ama":"Zhu J, Bailly A, Zwiewka M, et al. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. <i>Plant Cell</i>. 2016;28(4):930-948. doi:<a href=\"https://doi.org/10.1105/tpc.15.00726\">10.1105/tpc.15.00726</a>","short":"J. Zhu, A. Bailly, M. Zwiewka, V. Sovero, M. Di Donato, P. Ge, J. Oehri, B. Aryal, P. Hao, M. Linnert, N. Burgardt, C. Lücke, M. Weiwad, M. Michel, O. Weiergräber, S. Pollmann, E. Azzarello, S. Mancuso, N. Ferro, Y. Fukao, C. Hoffmann, R. Wedlich Söldner, J. Friml, C. Thomas, M. Geisler, Plant Cell 28 (2016) 930–948."},"doi":"10.1105/tpc.15.00726","publication_status":"published","date_published":"2016-04-01T00:00:00Z","oa_version":"Submitted Version","oa":1,"status":"public","month":"04","year":"2016","abstract":[{"lang":"eng","text":"Plant growth and architecture is regulated by the polar distribution of the hormone auxin. Polarity and flexibility of this process is provided by constant cycling of auxin transporter vesicles along actin filaments, coordinated by a positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic acid (NPA), counteracting the effect of auxin; however, underlying targets and mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis thaliana ABCB chaperone TWISTED DWARF1 (TWD1).We identify ACTIN7 as a relevant, although likely indirect, TWD1 interactor, and show TWD1-dependent regulation of actin filament organization and dynamics and that TWD1 is required for NPA-mediated actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence of efflux transporters, and as a consequence act7 and twd1 share developmental and physiological phenotypes indicative of defects in auxin transport. These can be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide evidence that TWD1 determines downstreamlocations of auxin efflux transporters by adjusting actin filament debundling and dynamizing processes and mediating NPA action on the latter. This function appears to be evolutionary conserved since TWD1 expression in budding yeast alters actin polarization and cell polarity and provides NPA sensitivity."}],"issue":"4","date_updated":"2021-01-12T06:49:24Z","_id":"1251","publist_id":"6078","quality_controlled":"1","volume":28,"publication":"Plant Cell","date_created":"2018-12-11T11:50:57Z","page":"930 - 948","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"type":"journal_article","title":"TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Society of Plant Biologists","day":"01","acknowledgement":" This work was supported by grants from the European Social Fund (CZ.1.07/2.3.00/20.0043), the Czech Science Foundation GAČR (GA13-40637S) to J.F. and M.Z., the Ministry of Education, Youth, and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) to M.Z., the Ministry for Higher Education and Research of Luxembourg (REC-LOCM-20140703) to C.T., the Partial Funding Program for Short Stays Abroad of CONICET Argentina (to N.I.B.), Swiss National Funds, the Pool de Recherche of the University of Fribourg, and the Novartis Foundation (all to M.G.). ","author":[{"last_name":"Zhu","first_name":"Jinsheng","full_name":"Zhu, Jinsheng"},{"last_name":"Bailly","first_name":"Aurélien","full_name":"Bailly, Aurélien"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"first_name":"Valpuri","last_name":"Sovero","full_name":"Sovero, Valpuri"},{"first_name":"Martin","last_name":"Di Donato","full_name":"Di Donato, Martin"},{"first_name":"Pei","last_name":"Ge","full_name":"Ge, Pei"},{"full_name":"Oehri, Jacqueline","last_name":"Oehri","first_name":"Jacqueline"},{"first_name":"Bibek","last_name":"Aryal","full_name":"Aryal, Bibek"},{"first_name":"Pengchao","last_name":"Hao","full_name":"Hao, Pengchao"},{"last_name":"Linnert","first_name":"Miriam","full_name":"Linnert, Miriam"},{"full_name":"Burgardt, Noelia","first_name":"Noelia","last_name":"Burgardt"},{"last_name":"Lücke","first_name":"Christian","full_name":"Lücke, Christian"},{"first_name":"Matthias","last_name":"Weiwad","full_name":"Weiwad, Matthias"},{"last_name":"Michel","first_name":"Max","full_name":"Michel, Max"},{"last_name":"Weiergräber","first_name":"Oliver","full_name":"Weiergräber, Oliver"},{"first_name":"Stephan","last_name":"Pollmann","full_name":"Pollmann, Stephan"},{"first_name":"Elisa","last_name":"Azzarello","full_name":"Azzarello, Elisa"},{"last_name":"Mancuso","first_name":"Stefano","full_name":"Mancuso, Stefano"},{"last_name":"Ferro","first_name":"Noel","full_name":"Ferro, Noel"},{"first_name":"Yoichiro","last_name":"Fukao","full_name":"Fukao, Yoichiro"},{"first_name":"Céline","last_name":"Hoffmann","full_name":"Hoffmann, Céline"},{"full_name":"Wedlich Söldner, Roland","first_name":"Roland","last_name":"Wedlich Söldner"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"full_name":"Thomas, Clément","first_name":"Clément","last_name":"Thomas"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"}]},{"oa_version":"Preprint","date_published":"2016-04-01T00:00:00Z","doi":"10.1090/proc/12812","publication_status":"published","citation":{"chicago":"Harker, Shaun, Hiroshi Kokubu, Konstantin Mischaikow, and Pawel Pilarczyk. “Inducing a Map on Homology from a Correspondence.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2016. <a href=\"https://doi.org/10.1090/proc/12812\">https://doi.org/10.1090/proc/12812</a>.","mla":"Harker, Shaun, et al. “Inducing a Map on Homology from a Correspondence.” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4, American Mathematical Society, 2016, pp. 1787–801, doi:<a href=\"https://doi.org/10.1090/proc/12812\">10.1090/proc/12812</a>.","ista":"Harker S, Kokubu H, Mischaikow K, Pilarczyk P. 2016. Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. 144(4), 1787–1801.","apa":"Harker, S., Kokubu, H., Mischaikow, K., &#38; Pilarczyk, P. (2016). Inducing a map on homology from a correspondence. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/12812\">https://doi.org/10.1090/proc/12812</a>","short":"S. Harker, H. Kokubu, K. Mischaikow, P. Pilarczyk, Proceedings of the American Mathematical Society 144 (2016) 1787–1801.","ama":"Harker S, Kokubu H, Mischaikow K, Pilarczyk P. Inducing a map on homology from a correspondence. <i>Proceedings of the American Mathematical Society</i>. 2016;144(4):1787-1801. doi:<a href=\"https://doi.org/10.1090/proc/12812\">10.1090/proc/12812</a>","ieee":"S. Harker, H. Kokubu, K. Mischaikow, and P. Pilarczyk, “Inducing a map on homology from a correspondence,” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4. American Mathematical Society, pp. 1787–1801, 2016."},"intvolume":"       144","main_file_link":[{"url":"https://arxiv.org/abs/1411.7563","open_access":"1"}],"scopus_import":"1","_id":"1252","arxiv":1,"issue":"4","abstract":[{"lang":"eng","text":"We study the homomorphism induced in homology by a closed correspondence between topological spaces, using projections from the graph of the correspondence to its domain and codomain. We provide assumptions under which the homomorphism induced by an outer approximation of a continuous map coincides with the homomorphism induced in homology by the map. In contrast to more classical results we do not require that the projection to the domain have acyclic preimages. Moreover, we show that it is possible to retrieve correct homological information from a correspondence even if some data is missing or perturbed. Finally, we describe an application to combinatorial maps that are either outer approximations of continuous maps or reconstructions of such maps from a finite set of data points."}],"date_updated":"2022-05-24T09:35:58Z","year":"2016","month":"04","ec_funded":1,"status":"public","publication_identifier":{"issn":["1088-6826"]},"oa":1,"type":"journal_article","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"publication":"Proceedings of the American Mathematical Society","date_created":"2018-12-11T11:50:57Z","page":"1787 - 1801","quality_controlled":"1","volume":144,"external_id":{"arxiv":["1411.7563"]},"article_processing_charge":"No","article_type":"original","publist_id":"6075","author":[{"first_name":"Shaun","last_name":"Harker","full_name":"Harker, Shaun"},{"first_name":"Hiroshi","last_name":"Kokubu","full_name":"Kokubu, Hiroshi"},{"first_name":"Konstantin","last_name":"Mischaikow","full_name":"Mischaikow, Konstantin"},{"first_name":"Pawel","last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel"}],"project":[{"grant_number":"622033","_id":"255F06BE-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps"}],"acknowledgement":"The authors gratefully acknowledge the support of the Lorenz Center which\r\nprovided an opportunity for us to discuss in depth the work of this paper. Research leading to these results has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Funda¸c˜ao para a Ciˆencia e a Tecnologia (FCT) in the framework of the research\r\nproject FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008),\r\nas well as from the People Programme (Marie Curie Actions) of the European\r\nUnion’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033 (supporting PP). The work of the first and third author has\r\nbeen partially supported by NSF grants NSF-DMS-0835621, 0915019, 1125174,\r\n1248071, and contracts from AFOSR and DARPA. The work of the second author\r\nwas supported by Grant-in-Aid for Scientific Research (No. 25287029), Ministry of\r\nEducation, Science, Technology, Culture and Sports, Japan.","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Mathematical Society","title":"Inducing a map on homology from a correspondence"},{"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"SaSi"}],"has_accepted_license":"1","page":"409 - 410","date_created":"2018-12-11T11:50:58Z","publication":"JAMA Psychiatry","external_id":{"pmid":["26963490"]},"volume":73,"quality_controlled":"1","publist_id":"6074","pubrep_id":"981","article_processing_charge":"No","author":[{"full_name":"Tsai, Lihuei","last_name":"Tsai","first_name":"Lihuei"},{"first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":601679,"file_id":"5278","checksum":"649aee381f30f7ef7e9efa912d41c2e3","creator":"system","access_level":"open_access","file_name":"IST-2018-981-v1+1_YNP150011_annotatedproof_FINAL.pdf","date_updated":"2020-07-14T12:44:41Z","date_created":"2018-12-12T10:17:24Z"}],"pmid":1,"day":"01","publisher":"American Medical Association","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"How MicroRNAs Are involved in splitting the mind","oa_version":"Submitted Version","date_published":"2016-04-01T00:00:00Z","publication_status":"published","doi":"10.1001/jamapsychiatry.2015.3144","intvolume":"        73","citation":{"ieee":"L. Tsai and S. Siegert, “How MicroRNAs Are involved in splitting the mind,” <i>JAMA Psychiatry</i>, vol. 73, no. 4. American Medical Association, pp. 409–410, 2016.","ama":"Tsai L, Siegert S. How MicroRNAs Are involved in splitting the mind. <i>JAMA Psychiatry</i>. 2016;73(4):409-410. doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">10.1001/jamapsychiatry.2015.3144</a>","short":"L. Tsai, S. Siegert, JAMA Psychiatry 73 (2016) 409–410.","chicago":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” <i>JAMA Psychiatry</i>. American Medical Association, 2016. <a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">https://doi.org/10.1001/jamapsychiatry.2015.3144</a>.","apa":"Tsai, L., &#38; Siegert, S. (2016). How MicroRNAs Are involved in splitting the mind. <i>JAMA Psychiatry</i>. American Medical Association. <a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">https://doi.org/10.1001/jamapsychiatry.2015.3144</a>","mla":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” <i>JAMA Psychiatry</i>, vol. 73, no. 4, American Medical Association, 2016, pp. 409–10, doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2015.3144\">10.1001/jamapsychiatry.2015.3144</a>.","ista":"Tsai L, Siegert S. 2016. How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. 73(4), 409–410."},"file_date_updated":"2020-07-14T12:44:41Z","scopus_import":"1","ddc":["576","610"],"_id":"1253","date_updated":"2024-02-14T12:07:22Z","abstract":[{"text":"This article provides an introduction to the role of microRNAs in the nervous system and outlines their potential involvement in the pathophysiology of schizophrenia, which is hypothesized to arise owing to environmental factors and genetic predisposition.","lang":"eng"}],"issue":"4","year":"2016","month":"04","status":"public","publication_identifier":{"issn":["2168-622X"]},"oa":1},{"publist_id":"6071","quality_controlled":"1","volume":25,"date_created":"2018-12-11T11:50:58Z","page":"116 - 124","publication":"Experimental Mathematics","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publisher":"Taylor and Francis","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Uniform expansivity outside a critical neighborhood in the quadratic family","acknowledgement":"AG and PP were partially supported by Abdus Salam International Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS, and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033. The  authors  gratefully  acknowledge  the  Department  of\r\nMathematics  of  Kyoto  University  for  providing  access\r\nto  their  server  for  conducting  computations  for  this\r\nproject.","day":"02","project":[{"grant_number":"622033","_id":"255F06BE-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps"}],"author":[{"full_name":"Golmakani, Ali","first_name":"Ali","last_name":"Golmakani"},{"last_name":"Luzzatto","first_name":"Stefano","full_name":"Luzzatto, Stefano"},{"first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel"}],"main_file_link":[{"url":"https://arxiv.org/abs/1504.00116","open_access":"1"}],"scopus_import":1,"intvolume":"        25","citation":{"short":"A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016) 116–124.","ama":"Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical neighborhood in the quadratic family. <i>Experimental Mathematics</i>. 2016;25(2):116-124. doi:<a href=\"https://doi.org/10.1080/10586458.2015.1048011\">10.1080/10586458.2015.1048011</a>","ieee":"A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside a critical neighborhood in the quadratic family,” <i>Experimental Mathematics</i>, vol. 25, no. 2. Taylor and Francis, pp. 116–124, 2016.","apa":"Golmakani, A., Luzzatto, S., &#38; Pilarczyk, P. (2016). Uniform expansivity outside a critical neighborhood in the quadratic family. <i>Experimental Mathematics</i>. Taylor and Francis. <a href=\"https://doi.org/10.1080/10586458.2015.1048011\">https://doi.org/10.1080/10586458.2015.1048011</a>","ista":"Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 25(2), 116–124.","mla":"Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” <i>Experimental Mathematics</i>, vol. 25, no. 2, Taylor and Francis, 2016, pp. 116–24, doi:<a href=\"https://doi.org/10.1080/10586458.2015.1048011\">10.1080/10586458.2015.1048011</a>.","chicago":"Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” <i>Experimental Mathematics</i>. Taylor and Francis, 2016. <a href=\"https://doi.org/10.1080/10586458.2015.1048011\">https://doi.org/10.1080/10586458.2015.1048011</a>."},"publication_status":"published","doi":"10.1080/10586458.2015.1048011","oa_version":"Preprint","date_published":"2016-04-02T00:00:00Z","status":"public","oa":1,"month":"04","ec_funded":1,"date_updated":"2021-01-12T06:49:25Z","issue":"2","abstract":[{"text":"We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/.","lang":"eng"}],"year":"2016","_id":"1254"},{"date_created":"2018-12-11T11:50:58Z","publication":"Royal Society Open Science","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"type":"journal_article","publist_id":"6070","pubrep_id":"704","volume":3,"quality_controlled":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","acknowledgement":"We thank Dietmar Schmucker for reading a draft of this manuscript and thank him and his group for\r\nhelpful discussions. We thank Barbara Hasert, Kevin Ferro and Manuel F. Talarico for technical support and helpful\r\ndiscussions. We also thank two anonymous reviewers for their comments. This study was supported by grants from the Volkswagen Stiftung (1/83 516 and AZ 86020: both to S.A.O.A.) and from the DFG priority programme 1399 ‘Host parasite coevolution’ (KU 1929/4-2 to R.P. and J.K.).","file":[{"date_created":"2018-12-12T10:14:01Z","date_updated":"2020-07-14T12:44:41Z","file_name":"IST-2016-704-v1+1_160138.full.pdf","access_level":"open_access","file_id":"5049","creator":"system","checksum":"c3cd84666c8dc0ce6a784f1c82c1cf68","file_size":627377,"content_type":"application/pdf","relation":"main_file"}],"author":[{"last_name":"Peuß","first_name":"Robert","full_name":"Peuß, Robert"},{"full_name":"Wensing, Kristina","last_name":"Wensing","first_name":"Kristina"},{"last_name":"Woestmann","first_name":"Luisa","full_name":"Woestmann, Luisa"},{"full_name":"Eggert, Hendrik","first_name":"Hendrik","last_name":"Eggert"},{"first_name":"Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","full_name":"Milutinovic, Barbara"},{"full_name":"Sroka, Marlene","last_name":"Sroka","first_name":"Marlene"},{"full_name":"Scharsack, Jörn","last_name":"Scharsack","first_name":"Jörn"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"last_name":"Armitage","first_name":"Sophie","full_name":"Armitage, Sophie"}],"title":"Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction","publisher":"Royal Society, The","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","doi":"10.1098/rsos.160138","date_published":"2016-04-01T00:00:00Z","oa_version":"Published Version","ddc":["576","592"],"file_date_updated":"2020-07-14T12:44:41Z","scopus_import":1,"citation":{"chicago":"Peuß, Robert, Kristina Wensing, Luisa Woestmann, Hendrik Eggert, Barbara Milutinovic, Marlene Sroka, Jörn Scharsack, Joachim Kurtz, and Sophie Armitage. “Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity, Behaviour and Reproduction.” <i>Royal Society Open Science</i>. Royal Society, The, 2016. <a href=\"https://doi.org/10.1098/rsos.160138\">https://doi.org/10.1098/rsos.160138</a>.","mla":"Peuß, Robert, et al. “Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity, Behaviour and Reproduction.” <i>Royal Society Open Science</i>, vol. 3, no. 4, 160138, Royal Society, The, 2016, doi:<a href=\"https://doi.org/10.1098/rsos.160138\">10.1098/rsos.160138</a>.","apa":"Peuß, R., Wensing, K., Woestmann, L., Eggert, H., Milutinovic, B., Sroka, M., … Armitage, S. (2016). Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. <i>Royal Society Open Science</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rsos.160138\">https://doi.org/10.1098/rsos.160138</a>","ista":"Peuß R, Wensing K, Woestmann L, Eggert H, Milutinovic B, Sroka M, Scharsack J, Kurtz J, Armitage S. 2016. Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. Royal Society Open Science. 3(4), 160138.","ieee":"R. Peuß <i>et al.</i>, “Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction,” <i>Royal Society Open Science</i>, vol. 3, no. 4. Royal Society, The, 2016.","ama":"Peuß R, Wensing K, Woestmann L, et al. Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. <i>Royal Society Open Science</i>. 2016;3(4). doi:<a href=\"https://doi.org/10.1098/rsos.160138\">10.1098/rsos.160138</a>","short":"R. Peuß, K. Wensing, L. Woestmann, H. Eggert, B. Milutinovic, M. Sroka, J. Scharsack, J. Kurtz, S. Armitage, Royal Society Open Science 3 (2016)."},"intvolume":"         3","year":"2016","date_updated":"2021-01-12T06:49:25Z","abstract":[{"text":"Down syndrome cell adhesion molecule 1 (Dscam1) has widereaching and vital neuronal functions although the role it plays in insect and crustacean immunity is less well understood. In this study, we combine different approaches to understand the roles that Dscam1 plays in fitness-related contexts in two model insect species. Contrary to our expectations, we found no short-term modulation of Dscam1 gene expression after haemocoelic or oral bacterial exposure in Tribolium castaneum, or after haemocoelic bacterial exposure in Drosophila melanogaster. Furthermore, RNAi-mediated Dscam1 knockdown and subsequent bacterial exposure did not reduce T. castaneum survival. However, Dscam1 knockdown in larvae resulted in adult locomotion defects, as well as dramatically reduced fecundity in males and females. We suggest that Dscam1 does not always play a straightforward role in immunity, but strongly influences behaviour and fecundity. This study takes a step towards understanding more about the role of this intriguing gene from different phenotypic perspectives.","lang":"eng"}],"issue":"4","_id":"1255","article_number":"160138","oa":1,"status":"public","month":"04"}]