[{"citation":{"chicago":"Rakusová, Hana, Matyas Fendrych, and Jiří Friml. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">https://doi.org/10.1016/j.pbi.2014.12.002</a>.","short":"H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015) 116–123.","ista":"Rakusová H, Fendrych M, Friml J. 2015. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 23(2), 116–123.","ieee":"H. Rakusová, M. Fendrych, and J. Friml, “Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants,” <i>Current Opinion in Plant Biology</i>, vol. 23, no. 2. Elsevier, pp. 116–123, 2015.","ama":"Rakusová H, Fendrych M, Friml J. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. <i>Current Opinion in Plant Biology</i>. 2015;23(2):116-123. doi:<a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">10.1016/j.pbi.2014.12.002</a>","apa":"Rakusová, H., Fendrych, M., &#38; Friml, J. (2015). Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">https://doi.org/10.1016/j.pbi.2014.12.002</a>","mla":"Rakusová, Hana, et al. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” <i>Current Opinion in Plant Biology</i>, vol. 23, no. 2, Elsevier, 2015, pp. 116–23, doi:<a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">10.1016/j.pbi.2014.12.002</a>."},"author":[{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"},{"orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","last_name":"Fendrych"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T06:54:15Z","year":"2015","day":"01","publication":"Current Opinion in Plant Biology","ec_funded":1,"title":"Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants","department":[{"_id":"JiFr"}],"_id":"1944","doi":"10.1016/j.pbi.2014.12.002","language":[{"iso":"eng"}],"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); the Agency for Innovation by Science and Technology (IWT) (predoctoral fellowship to H.R.); and the People Programme (Marie Curie Actions) of the European Union","publication_status":"published","date_published":"2015-02-01T00:00:00Z","page":"116 - 123","issue":"2","volume":23,"publisher":"Elsevier","intvolume":"        23","scopus_import":1,"publist_id":"5140","month":"02","date_created":"2018-12-11T11:54:51Z","status":"public"},{"quality_controlled":"1","author":[{"last_name":"Gupta","first_name":"Ashutosh","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Arjun","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","full_name":"Samanta, Roopsha","last_name":"Samanta","first_name":"Roopsha"},{"id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten","last_name":"Tarrach","first_name":"Thorsten"}],"citation":{"chicago":"Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta, and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44. ACM, 2015. <a href=\"https://doi.org/10.1145/2676726.2677008\">https://doi.org/10.1145/2676726.2677008</a>.","short":"A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM, 2015, pp. 433–444.","ista":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct representation of concurrent trace sets. POPL: Principles of Programming Languages, 433–444.","ieee":"A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct representation of concurrent trace sets,” presented at the POPL: Principles of Programming Languages, Mumbai, India, 2015, pp. 433–444.","ama":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation of concurrent trace sets. In: ACM; 2015:433-444. doi:<a href=\"https://doi.org/10.1145/2676726.2677008\">10.1145/2676726.2677008</a>","mla":"Gupta, Ashutosh, et al. <i>Succinct Representation of Concurrent Trace Sets</i>. ACM, 2015, pp. 433–44, doi:<a href=\"https://doi.org/10.1145/2676726.2677008\">10.1145/2676726.2677008</a>.","apa":"Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., &#38; Tarrach, T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented at the POPL: Principles of Programming Languages, Mumbai, India: ACM. <a href=\"https://doi.org/10.1145/2676726.2677008\">https://doi.org/10.1145/2676726.2677008</a>"},"year":"2015","ddc":["005"],"oa":1,"_id":"1992","title":"Succinct representation of concurrent trace sets","publication_status":"published","abstract":[{"text":"We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings.\r\n\r\nWe claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula.","lang":"eng"}],"pubrep_id":"317","publisher":"ACM","file_date_updated":"2020-07-14T12:45:22Z","publist_id":"5091","status":"public","date_created":"2018-12-11T11:55:05Z","month":"01","conference":{"name":"POPL: Principles of Programming Languages","end_date":"2015-01-17","location":"Mumbai, India","start_date":"2015-01-15"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","type":"conference","date_updated":"2021-01-12T06:54:33Z","oa_version":"Submitted Version","doi":"10.1145/2676726.2677008","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"ToHe"}],"page":"433 - 444","date_published":"2015-01-15T00:00:00Z","file":[{"file_id":"5314","date_updated":"2020-07-14T12:45:22Z","access_level":"open_access","file_name":"IST-2015-317-v1+1_author_version.pdf","checksum":"f0d4395b600f410a191256ac0b73af32","date_created":"2018-12-12T10:17:56Z","relation":"main_file","file_size":399462,"content_type":"application/pdf","creator":"system"}],"publication_identifier":{"isbn":["978-1-4503-3300-9"]},"scopus_import":1},{"language":[{"iso":"eng"}],"doi":"10.1098/rspb.2014.1976","department":[{"_id":"SyCr"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"acknowledgement":"Funding was obtained by the German Research Foundation (CR 118–2) and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank Line V. Ugelvig for help with ant collection and statistical discussion, Xavier Espadaler for detailed information on the ant collection site, Birgit Lautenschläger for the electron microscopy images and Eva Sixt for ant drawings. We further thank Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization and immune gene primer development, Paul Schmid-Hempel for discussion, and Line V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript. S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments; M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with intense contributions of A.V.G. and S.T.; all authors approved the manuscript.","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","type":"journal_article","date_updated":"2023-02-23T14:06:41Z","oa_version":"Submitted Version","publication_identifier":{"issn":["0962-8452"],"eissn":["1471-2954"]},"scopus_import":"1","date_published":"2015-01-22T00:00:00Z","external_id":{"pmid":["25473011"]},"oa":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9740"}]},"_id":"1993","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","title":"Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","pmid":1,"publication_status":"published","abstract":[{"lang":"eng","text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens. "}],"project":[{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071"},{"name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias","first_name":"Matthias","last_name":"Konrad"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse"},{"first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"quality_controlled":"1","citation":{"ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1799), 20141976.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society, 2015. <a href=\"https://doi.org/10.1098/rspb.2014.1976\">https://doi.org/10.1098/rspb.2014.1976</a>.","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1799. The Royal Society, 2015.","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2015;282(1799). doi:<a href=\"https://doi.org/10.1098/rspb.2014.1976\">10.1098/rspb.2014.1976</a>","mla":"Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1799, 20141976, The Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rspb.2014.1976\">10.1098/rspb.2014.1976</a>.","apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2015). Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2014.1976\">https://doi.org/10.1098/rspb.2014.1976</a>"},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/","open_access":"1"}],"year":"2015","publist_id":"5090","intvolume":"       282","article_number":"20141976","status":"public","date_created":"2018-12-11T11:55:06Z","month":"01","issue":"1799","volume":282,"article_type":"original","publisher":"The Royal Society"},{"scopus_import":1,"publist_id":"5082","status":"public","month":"05","date_created":"2018-12-11T11:55:07Z","issue":"May-June","volume":"68/Part 2","page":"285 - 296","date_published":"2015-05-01T00:00:00Z","publisher":"Elsevier","department":[{"_id":"CaUh"}],"_id":"1997","oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jsc.2014.09.014","publication":"Journal of Symbolic Computation","title":"The three-state toric homogeneous Markov chain model has Markov degree two","abstract":[{"text":"We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials.","lang":"eng"}],"publication_status":"published","author":[{"full_name":"Noren, Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87","first_name":"Patrik","last_name":"Noren"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June, Elsevier, 2015, pp. 285–96, doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>.","apa":"Noren, P. (2015). The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>","ama":"Noren P. The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. 2015;68/Part 2(May-June):285-296. doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>","ieee":"P. Noren, “The three-state toric homogeneous Markov chain model has Markov degree two,” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June. Elsevier, pp. 285–296, 2015.","ista":"Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.","short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.","chicago":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>."},"main_file_link":[{"url":"http://arxiv.org/abs/1207.0077","open_access":"1"}],"year":"2015","day":"01","oa_version":"Preprint","type":"journal_article","date_updated":"2021-01-12T06:54:35Z"},{"abstract":[{"lang":"eng","text":"The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. "}],"publication_status":"published","title":"The monotone secant conjecture in the real Schubert calculus","publication":"Experimental Mathematics","_id":"2006","oa":1,"year":"2015","citation":{"apa":"Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., &#38; Teitler, Z. (2015). The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>","mla":"Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>, vol. 24, no. 3, Taylor &#38; Francis, 2015, pp. 261–69, doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>.","chicago":"Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>. Taylor &#38; Francis, 2015. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>.","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269.","ista":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 24(3), 261–269.","ama":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. 2015;24(3):261-269. doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>","ieee":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler, “The monotone secant conjecture in the real Schubert calculus,” <i>Experimental Mathematics</i>, vol. 24, no. 3. Taylor &#38; Francis, pp. 261–269, 2015."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.3436"}],"quality_controlled":"1","author":[{"first_name":"Nicolas","last_name":"Hein","full_name":"Hein, Nicolas"},{"full_name":"Hillar, Christopher","last_name":"Hillar","first_name":"Christopher"},{"full_name":"Martin Del Campo Sanchez, Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","last_name":"Martin Del Campo Sanchez","first_name":"Abraham"},{"full_name":"Sottile, Frank","first_name":"Frank","last_name":"Sottile"},{"first_name":"Zach","last_name":"Teitler","full_name":"Teitler, Zach"}],"month":"06","date_created":"2018-12-11T11:55:10Z","status":"public","intvolume":"        24","publist_id":"5070","publisher":"Taylor & Francis","issue":"3","volume":24,"department":[{"_id":"CaUh"}],"language":[{"iso":"eng"}],"doi":"10.1080/10586458.2014.980044","oa_version":"Preprint","date_updated":"2021-01-12T06:54:40Z","type":"journal_article","day":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","scopus_import":1,"date_published":"2015-06-23T00:00:00Z","page":"261 - 269"},{"department":[{"_id":"CaUh"}],"language":[{"iso":"eng"}],"doi":"10.1111/sjos.12139","acknowledgement":"Part of the material presented here was contained in the PhD thesis of the first author to which the second author and Thomas Richardson were advisers. The authors wish to thank him for several comments and suggestions. We also thank the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1 uses the idea of Olga Klimova, to whom the authors are also indebted. The second author was supported in part by Grant K-106154 from the Hungarian National Scientific Research Fund (OTKA).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Preprint","type":"journal_article","date_updated":"2021-01-12T06:54:41Z","scopus_import":1,"page":"832 - 847","date_published":"2015-09-01T00:00:00Z","_id":"2008","oa":1,"title":"Iterative scaling in curved exponential families","publication":"Scandinavian Journal of Statistics","abstract":[{"text":"The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","author":[{"first_name":"Anna","last_name":"Klimova","id":"31934120-F248-11E8-B48F-1D18A9856A87","full_name":"Klimova, Anna"},{"last_name":"Rudas","first_name":"Tamás","full_name":"Rudas, Tamás"}],"citation":{"short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.","chicago":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>.","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","ieee":"A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3. Wiley, pp. 832–847, 2015.","ama":"Klimova A, Rudas T. Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. 2015;42(3):832-847. doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>","apa":"Klimova, A., &#38; Rudas, T. (2015). Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. Wiley. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>","mla":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3, Wiley, 2015, pp. 832–47, doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3282"}],"year":"2015","publist_id":"5068","intvolume":"        42","status":"public","month":"09","date_created":"2018-12-11T11:55:11Z","volume":42,"issue":"3","publisher":"Wiley"},{"publication":"Computational Statistics & Data Analysis","title":"Faithfulness and learning hypergraphs from discrete distributions","_id":"2014","department":[{"_id":"CaUh"}],"language":[{"iso":"eng"}],"oa":1,"doi":"10.1016/j.csda.2015.01.017","abstract":[{"lang":"eng","text":"The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association."}],"publication_status":"published","citation":{"ieee":"A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs from discrete distributions,” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7. Elsevier, pp. 57–72, 2015.","ama":"Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. 2015;87(7):57-72. doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>","short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics &#38; Data Analysis 87 (2015) 57–72.","chicago":"Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>.","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics &#38; Data Analysis. 87(7), 57–72.","mla":"Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7, Elsevier, 2015, pp. 57–72, doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>.","apa":"Klimova, A., Uhler, C., &#38; Rudas, T. (2015). Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>"},"main_file_link":[{"url":"http://arxiv.org/abs/1404.6617","open_access":"1"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Klimova, Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Klimova"},{"first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216"},{"full_name":"Rudas, Tamás","first_name":"Tamás","last_name":"Rudas"}],"oa_version":"Preprint","type":"journal_article","date_updated":"2021-01-12T06:54:43Z","year":"2015","day":"01","intvolume":"        87","scopus_import":1,"publist_id":"5062","month":"07","date_created":"2018-12-11T11:55:13Z","status":"public","date_published":"2015-07-01T00:00:00Z","volume":87,"page":"57 - 72","issue":"7","publisher":"Elsevier"},{"title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","publication":"Biochimica et Biophysica Acta - Molecular Cell Research","oa":1,"ddc":["570"],"_id":"2025","publication_status":"published","abstract":[{"lang":"eng","text":"Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins."}],"citation":{"mla":"Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>.","apa":"Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D. E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>","ista":"Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(1), 144–156.","chicago":"Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>.","short":"D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus, J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 144–156.","ama":"Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. 2015;1853(1):144-156. doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>","ieee":"D. Kawada <i>et al.</i>, “The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins,” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015."},"quality_controlled":"1","author":[{"full_name":"Kawada, Daiki","last_name":"Kawada","first_name":"Daiki"},{"first_name":"Hiromu","last_name":"Kobayashi","full_name":"Kobayashi, Hiromu"},{"full_name":"Tomita, Tsuyoshi","last_name":"Tomita","first_name":"Tsuyoshi"},{"last_name":"Nakata","first_name":"Eisuke","full_name":"Nakata, Eisuke"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"last_name":"Siekhaus","first_name":"Daria E","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Junko","last_name":"Toshima","full_name":"Toshima, Junko"},{"last_name":"Toshimaa","first_name":"Jiro","full_name":"Toshimaa, Jiro"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2015","intvolume":"      1853","publist_id":"5047","date_created":"2018-12-11T11:55:17Z","month":"01","status":"public","issue":"1","volume":1853,"pubrep_id":"615","file_date_updated":"2020-07-14T12:45:25Z","publisher":"Elsevier","doi":"10.1016/j.bbamcr.2014.10.009","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"DaSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_updated":"2021-01-12T06:54:48Z","oa_version":"Submitted Version","day":"01","scopus_import":1,"date_published":"2015-01-01T00:00:00Z","file":[{"date_created":"2018-12-12T10:12:18Z","relation":"main_file","file_size":926685,"creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:45:25Z","file_id":"4936","access_level":"open_access","checksum":"5bb328edebb6a91337cadd7d63f961b7","file_name":"IST-2016-615-v1+1_BBAMCR.pdf"}],"page":"144 - 156"},{"publisher":"Elsevier","date_published":"2015-01-01T00:00:00Z","page":"1 - 11","volume":106,"issue":"1","month":"01","date_created":"2018-12-11T11:55:18Z","status":"public","intvolume":"       106","scopus_import":1,"publist_id":"5042","oa_version":"Preprint","type":"journal_article","date_updated":"2021-01-12T06:54:51Z","year":"2015","day":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.2481"}],"citation":{"mla":"Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” <i>Computers and Fluids</i>, vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>.","apa":"Shi, L., Rampp, M., Hof, B., &#38; Avila, M. (2015). A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. <i>Computers and Fluids</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>","ieee":"L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow,” <i>Computers and Fluids</i>, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.","ama":"Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. <i>Computers and Fluids</i>. 2015;106(1):1-11. doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>","ista":"Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 106(1), 1–11.","short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.","chicago":"Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” <i>Computers and Fluids</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>."},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","full_name":"Shi, Liang","last_name":"Shi","first_name":"Liang"},{"last_name":"Rampp","first_name":"Markus","full_name":"Rampp, Markus"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"abstract":[{"text":"A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes.","lang":"eng"}],"publication_status":"published","publication":"Computers and Fluids","title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","_id":"2030","department":[{"_id":"BjHo"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.compfluid.2014.09.021"},{"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"abstract":[{"text":"Opacity is a generic security property, that has been defined on (non-probabilistic) transition systems and later on Markov chains with labels. For a secret predicate, given as a subset of runs, and a function describing the view of an external observer, the value of interest for opacity is a measure of the set of runs disclosing the secret. We extend this definition to the richer framework of Markov decision processes, where non-deterministicchoice is combined with probabilistic transitions, and we study related decidability problems with partial or complete observation hypotheses for the schedulers. We prove that all questions are decidable with complete observation and ω-regular secrets. With partial observation, we prove that all quantitative questions are undecidable but the question whether a system is almost surely non-opaquebecomes decidable for a restricted class of ω-regular secrets, as well as for all ω-regular secrets under finite-memory schedulers.","lang":"eng"}],"publication_status":"published","publication":" Information Processing Letters","title":"Probabilistic opacity for Markov decision processes","_id":"2034","oa":1,"year":"2015","main_file_link":[{"url":"http://arxiv.org/abs/1407.4225","open_access":"1"}],"citation":{"apa":"Bérard, B., Chatterjee, K., &#38; Sznajder, N. (2015). Probabilistic opacity for Markov decision processes. <i> Information Processing Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">https://doi.org/10.1016/j.ipl.2014.09.001</a>","mla":"Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.” <i> Information Processing Letters</i>, vol. 115, no. 1, Elsevier, 2015, pp. 52–59, doi:<a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">10.1016/j.ipl.2014.09.001</a>.","ista":"Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov decision processes.  Information Processing Letters. 115(1), 52–59.","chicago":"Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic Opacity for Markov Decision Processes.” <i> Information Processing Letters</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">https://doi.org/10.1016/j.ipl.2014.09.001</a>.","short":"B. Bérard, K. Chatterjee, N. Sznajder,  Information Processing Letters 115 (2015) 52–59.","ama":"Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision processes. <i> Information Processing Letters</i>. 2015;115(1):52-59. doi:<a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">10.1016/j.ipl.2014.09.001</a>","ieee":"B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov decision processes,” <i> Information Processing Letters</i>, vol. 115, no. 1. Elsevier, pp. 52–59, 2015."},"author":[{"last_name":"Bérard","first_name":"Béatrice","full_name":"Bérard, Béatrice"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Nathalie","last_name":"Sznajder","full_name":"Sznajder, Nathalie"}],"quality_controlled":"1","month":"01","date_created":"2018-12-11T11:55:20Z","status":"public","intvolume":"       115","publist_id":"5025","publisher":"Elsevier","issue":"1","volume":115,"ec_funded":1,"department":[{"_id":"KrCh"}],"doi":"10.1016/j.ipl.2014.09.001","language":[{"iso":"eng"}],"oa_version":"Preprint","date_updated":"2021-01-12T06:54:52Z","type":"journal_article","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"date_published":"2015-01-01T00:00:00Z","page":"52 - 59"},{"date_updated":"2021-01-12T06:54:53Z","type":"journal_article","oa_version":"Published Version","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the Polish National Science Center under Grant No. N201 419639.","ec_funded":1,"doi":"10.1007/s10208-014-9223-y","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"has_accepted_license":"1","date_published":"2015-10-01T00:00:00Z","file":[{"access_level":"open_access","checksum":"3566f3a8b0c1bc550e62914a88c584ff","file_name":"IST-2016-486-v1+1_s10208-014-9223-y.pdf","file_id":"4670","date_updated":"2020-07-14T12:45:26Z","file_size":1317546,"content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:08:10Z","relation":"main_file"}],"page":"1213 - 1244","scopus_import":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2015","citation":{"ista":"Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.","short":"H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics 15 (2015) 1213–1244.","chicago":"Edelsbrunner, Herbert, Grzegorz Jablonski, and Marian Mrozek. “The Persistent Homology of a Self-Map.” <i>Foundations of Computational Mathematics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10208-014-9223-y\">https://doi.org/10.1007/s10208-014-9223-y</a>.","ieee":"H. Edelsbrunner, G. Jablonski, and M. Mrozek, “The persistent homology of a self-map,” <i>Foundations of Computational Mathematics</i>, vol. 15, no. 5. Springer, pp. 1213–1244, 2015.","ama":"Edelsbrunner H, Jablonski G, Mrozek M. The persistent homology of a self-map. <i>Foundations of Computational Mathematics</i>. 2015;15(5):1213-1244. doi:<a href=\"https://doi.org/10.1007/s10208-014-9223-y\">10.1007/s10208-014-9223-y</a>","apa":"Edelsbrunner, H., Jablonski, G., &#38; Mrozek, M. (2015). The persistent homology of a self-map. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-014-9223-y\">https://doi.org/10.1007/s10208-014-9223-y</a>","mla":"Edelsbrunner, Herbert, et al. “The Persistent Homology of a Self-Map.” <i>Foundations of Computational Mathematics</i>, vol. 15, no. 5, Springer, 2015, pp. 1213–44, doi:<a href=\"https://doi.org/10.1007/s10208-014-9223-y\">10.1007/s10208-014-9223-y</a>."},"author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner"},{"first_name":"Grzegorz","last_name":"Jablonski","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","full_name":"Jablonski, Grzegorz","orcid":"0000-0002-3536-9866"},{"full_name":"Mrozek, Marian","first_name":"Marian","last_name":"Mrozek"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","grant_number":"318493"}],"publication_status":"published","abstract":[{"text":"Considering a continuous self-map and the induced endomorphism on homology, we study the eigenvalues and eigenspaces of the latter. Taking a filtration of representations, we define the persistence of the eigenspaces, effectively introducing a hierarchical organization of the map. The algorithm that computes this information for a finite sample is proved to be stable, and to give the correct answer for a sufficiently dense sample. Results computed with an implementation of the algorithm provide evidence of its practical utility.\r\n","lang":"eng"}],"title":"The persistent homology of a self-map","publication":"Foundations of Computational Mathematics","ddc":["000"],"oa":1,"_id":"2035","file_date_updated":"2020-07-14T12:45:26Z","publisher":"Springer","issue":"5","volume":15,"pubrep_id":"486","date_created":"2018-12-11T11:55:20Z","month":"10","status":"public","intvolume":"        15","publist_id":"5022"},{"_id":"13392","pmid":1,"title":"Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks","publication":"Nature Nanotechnology","abstract":[{"text":"The chemical behaviour of molecules can be significantly modified by confinement to volumes comparable to the dimensions of the molecules. Although such confined spaces can be found in various nanostructured materials, such as zeolites, nanoporous organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of molecules in and out of these materials has greatly hampered studying the effect of confinement on their physicochemical properties. Here, we show that this diffusion limitation can be overcome by reversibly creating and destroying confined environments by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals functionalized with light-responsive ligands that readily self-assemble and trap various molecules from the surrounding bulk solution. Once trapped, these molecules can undergo chemical reactions with increased rates and with stereoselectivities significantly different from those in bulk solution. Illumination with visible light disassembles these nanoflasks, releasing the product in solution and thereby establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying chemical reactivities in confined environments and for synthesizing molecules that are otherwise hard to achieve in bulk solution.","lang":"eng"}],"publication_status":"published","extern":"1","author":[{"first_name":"Hui","last_name":"Zhao","full_name":"Zhao, Hui"},{"full_name":"Sen, Soumyo","last_name":"Sen","first_name":"Soumyo"},{"full_name":"Udayabhaskararao, T.","last_name":"Udayabhaskararao","first_name":"T."},{"full_name":"Sawczyk, Michał","last_name":"Sawczyk","first_name":"Michał"},{"full_name":"Kučanda, Kristina","last_name":"Kučanda","first_name":"Kristina"},{"full_name":"Manna, Debasish","first_name":"Debasish","last_name":"Manna"},{"first_name":"Pintu K.","last_name":"Kundu","full_name":"Kundu, Pintu K."},{"full_name":"Lee, Ji-Woong","last_name":"Lee","first_name":"Ji-Woong"},{"full_name":"Král, Petr","last_name":"Král","first_name":"Petr"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"}],"quality_controlled":"1","citation":{"ama":"Zhao H, Sen S, Udayabhaskararao T, et al. Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. <i>Nature Nanotechnology</i>. 2015;11:82-88. doi:<a href=\"https://doi.org/10.1038/nnano.2015.256\">10.1038/nnano.2015.256</a>","ieee":"H. Zhao <i>et al.</i>, “Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks,” <i>Nature Nanotechnology</i>, vol. 11. Springer Nature, pp. 82–88, 2015.","short":"H. Zhao, S. Sen, T. Udayabhaskararao, M. Sawczyk, K. Kučanda, D. Manna, P.K. Kundu, J.-W. Lee, P. Král, R. Klajn, Nature Nanotechnology 11 (2015) 82–88.","chicago":"Zhao, Hui, Soumyo Sen, T. Udayabhaskararao, Michał Sawczyk, Kristina Kučanda, Debasish Manna, Pintu K. Kundu, Ji-Woong Lee, Petr Král, and Rafal Klajn. “Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.” <i>Nature Nanotechnology</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nnano.2015.256\">https://doi.org/10.1038/nnano.2015.256</a>.","ista":"Zhao H, Sen S, Udayabhaskararao T, Sawczyk M, Kučanda K, Manna D, Kundu PK, Lee J-W, Král P, Klajn R. 2015. Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. 11, 82–88.","mla":"Zhao, Hui, et al. “Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.” <i>Nature Nanotechnology</i>, vol. 11, Springer Nature, 2015, pp. 82–88, doi:<a href=\"https://doi.org/10.1038/nnano.2015.256\">10.1038/nnano.2015.256</a>.","apa":"Zhao, H., Sen, S., Udayabhaskararao, T., Sawczyk, M., Kučanda, K., Manna, D., … Klajn, R. (2015). Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. <i>Nature Nanotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nnano.2015.256\">https://doi.org/10.1038/nnano.2015.256</a>"},"year":"2015","intvolume":"        11","status":"public","month":"11","date_created":"2023-08-01T09:44:04Z","volume":11,"publisher":"Springer Nature","article_type":"original","language":[{"iso":"eng"}],"doi":"10.1038/nnano.2015.256","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"23","oa_version":"None","type":"journal_article","date_updated":"2023-08-07T12:55:46Z","scopus_import":"1","publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"page":"82-88","external_id":{"pmid":["26595335"]},"keyword":["Electrical and Electronic Engineering","Condensed Matter Physics","General Materials Science","Biomedical Engineering","Atomic and Molecular Physics","and Optics","Bioengineering"],"date_published":"2015-11-23T00:00:00Z"},{"doi":"10.1002/anie.201502419","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","oa_version":"None","type":"journal_article","date_updated":"2023-08-07T12:58:29Z","day":"01","scopus_import":"1","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"keyword":["General Chemistry","Catalysis"],"external_id":{"pmid":["25959725"]},"date_published":"2015-10-01T00:00:00Z","page":"12394-12397","pmid":1,"title":"Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes","publication":"Angewandte Chemie International Edition","_id":"13393","abstract":[{"text":"Precise control of the self-assembly of selected components within complex mixtures is a challenging goal whose realization is important for fabricating novel nanomaterials. Herein we show that by decorating the surfaces of metallic nanoparticles with differently substituted azobenzenes, it is possible to modulate the wavelength of light at which the self-assembly of these nanoparticles is induced. Exposing a mixture of two types of nanoparticles, each functionalized with a different azobenzene, to UV or blue light induces the selective self-assembly of only one type of nanoparticles. Irradiation with the other wavelength triggers the disassembly of the aggregates, and the simultaneous self-assembly of nanoparticles of the other type. By placing both types of azobenzenes on the same nanoparticles, we created unique materials (“frustrated” nanoparticles) whose self-assembly is induced irrespective of the wavelength of the incident light.","lang":"eng"}],"publication_status":"published","citation":{"ista":"Manna D, Udayabhaskararao T, Zhao H, Klajn R. 2015. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. 54(42), 12394–12397.","chicago":"Manna, Debasish, Thumu Udayabhaskararao, Hui Zhao, and Rafal Klajn. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” <i>Angewandte Chemie International Edition</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/anie.201502419\">https://doi.org/10.1002/anie.201502419</a>.","short":"D. Manna, T. Udayabhaskararao, H. Zhao, R. Klajn, Angewandte Chemie International Edition 54 (2015) 12394–12397.","ieee":"D. Manna, T. Udayabhaskararao, H. Zhao, and R. Klajn, “Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes,” <i>Angewandte Chemie International Edition</i>, vol. 54, no. 42. Wiley, pp. 12394–12397, 2015.","ama":"Manna D, Udayabhaskararao T, Zhao H, Klajn R. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. <i>Angewandte Chemie International Edition</i>. 2015;54(42):12394-12397. doi:<a href=\"https://doi.org/10.1002/anie.201502419\">10.1002/anie.201502419</a>","apa":"Manna, D., Udayabhaskararao, T., Zhao, H., &#38; Klajn, R. (2015). Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201502419\">https://doi.org/10.1002/anie.201502419</a>","mla":"Manna, Debasish, et al. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” <i>Angewandte Chemie International Edition</i>, vol. 54, no. 42, Wiley, 2015, pp. 12394–97, doi:<a href=\"https://doi.org/10.1002/anie.201502419\">10.1002/anie.201502419</a>."},"quality_controlled":"1","author":[{"full_name":"Manna, Debasish","first_name":"Debasish","last_name":"Manna"},{"first_name":"Thumu","last_name":"Udayabhaskararao","full_name":"Udayabhaskararao, Thumu"},{"first_name":"Hui","last_name":"Zhao","full_name":"Zhao, Hui"},{"first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}],"extern":"1","year":"2015","intvolume":"        54","month":"10","date_created":"2023-08-01T09:44:19Z","status":"public","volume":54,"issue":"42","article_type":"original","publisher":"Wiley"},{"date_published":"2015-07-20T00:00:00Z","external_id":{"pmid":["26201741"]},"keyword":["General Chemical Engineering","General Chemistry"],"page":"646-652","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"scopus_import":"1","type":"journal_article","date_updated":"2023-08-07T13:00:15Z","oa_version":"None","day":"20","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/nchem.2303","language":[{"iso":"eng"}],"publisher":"Springer Nature","article_type":"original","volume":7,"date_created":"2023-08-01T09:44:33Z","month":"07","status":"public","intvolume":"         7","year":"2015","citation":{"apa":"Kundu, P. K., Samanta, D., Leizrowice, R., Margulis, B., Zhao, H., Börner, M., … Klajn, R. (2015). Light-controlled self-assembly of non-photoresponsive nanoparticles. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nchem.2303\">https://doi.org/10.1038/nchem.2303</a>","mla":"Kundu, Pintu K., et al. “Light-Controlled Self-Assembly of Non-Photoresponsive Nanoparticles.” <i>Nature Chemistry</i>, vol. 7, Springer Nature, 2015, pp. 646–52, doi:<a href=\"https://doi.org/10.1038/nchem.2303\">10.1038/nchem.2303</a>.","ieee":"P. K. Kundu <i>et al.</i>, “Light-controlled self-assembly of non-photoresponsive nanoparticles,” <i>Nature Chemistry</i>, vol. 7. Springer Nature, pp. 646–652, 2015.","ama":"Kundu PK, Samanta D, Leizrowice R, et al. Light-controlled self-assembly of non-photoresponsive nanoparticles. <i>Nature Chemistry</i>. 2015;7:646-652. doi:<a href=\"https://doi.org/10.1038/nchem.2303\">10.1038/nchem.2303</a>","chicago":"Kundu, Pintu K., Dipak Samanta, Ron Leizrowice, Baruch Margulis, Hui Zhao, Martin Börner, T. Udayabhaskararao, Debasish Manna, and Rafal Klajn. “Light-Controlled Self-Assembly of Non-Photoresponsive Nanoparticles.” <i>Nature Chemistry</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nchem.2303\">https://doi.org/10.1038/nchem.2303</a>.","short":"P.K. Kundu, D. Samanta, R. Leizrowice, B. Margulis, H. Zhao, M. Börner, T. Udayabhaskararao, D. Manna, R. Klajn, Nature Chemistry 7 (2015) 646–652.","ista":"Kundu PK, Samanta D, Leizrowice R, Margulis B, Zhao H, Börner M, Udayabhaskararao T, Manna D, Klajn R. 2015. Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. 7, 646–652."},"author":[{"last_name":"Kundu","first_name":"Pintu K.","full_name":"Kundu, Pintu K."},{"last_name":"Samanta","first_name":"Dipak","full_name":"Samanta, Dipak"},{"full_name":"Leizrowice, Ron","first_name":"Ron","last_name":"Leizrowice"},{"full_name":"Margulis, Baruch","last_name":"Margulis","first_name":"Baruch"},{"first_name":"Hui","last_name":"Zhao","full_name":"Zhao, Hui"},{"last_name":"Börner","first_name":"Martin","full_name":"Börner, Martin"},{"first_name":"T.","last_name":"Udayabhaskararao","full_name":"Udayabhaskararao, T."},{"full_name":"Manna, Debasish","last_name":"Manna","first_name":"Debasish"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn"}],"extern":"1","quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"The ability to guide the assembly of nanosized objects reversibly with external stimuli, in particular light, is of fundamental importance, and it contributes to the development of applications as diverse as nanofabrication and controlled drug delivery. However, all the systems described to date are based on nanoparticles (NPs) that are inherently photoresponsive, which makes their preparation cumbersome and can markedly hamper their performance. Here we describe a conceptually new methodology to assemble NPs reversibly using light that does not require the particles to be functionalized with light-responsive ligands. Our strategy is based on the use of a photoswitchable medium that responds to light in such a way that it modulates the interparticle interactions. NP assembly proceeds quantitatively and without apparent fatigue, both in solution and in gels. Exposing the gels to light in a spatially controlled manner allowed us to draw images that spontaneously disappeared after a specific period of time."}],"publication":"Nature Chemistry","title":"Light-controlled self-assembly of non-photoresponsive nanoparticles","pmid":1,"_id":"13394"},{"oa_version":"Published Version","date_updated":"2023-08-07T13:01:53Z","type":"journal_article","day":"18","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1039/c4cc08541h","language":[{"iso":"eng"}],"keyword":["Materials Chemistry","Metals and Alloys","Surfaces","Coatings and Films","General Chemistry","Ceramics and Composites","Electronic","Optical and Magnetic Materials","Catalysis"],"external_id":{"pmid":["25417754"]},"date_published":"2015-11-18T00:00:00Z","page":"2036-2039","scopus_import":"1","publication_identifier":{"eissn":["1364-548X"],"issn":["1359-7345"]},"year":"2015","citation":{"mla":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” <i>Chemical Communications</i>, vol. 51, no. 11, Royal Society of Chemistry, 2015, pp. 2036–39, doi:<a href=\"https://doi.org/10.1039/c4cc08541h\">10.1039/c4cc08541h</a>.","apa":"Lee, J.-W., &#38; Klajn, R. (2015). Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. <i>Chemical Communications</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c4cc08541h\">https://doi.org/10.1039/c4cc08541h</a>","short":"J.-W. Lee, R. Klajn, Chemical Communications 51 (2015) 2036–2039.","chicago":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” <i>Chemical Communications</i>. Royal Society of Chemistry, 2015. <a href=\"https://doi.org/10.1039/c4cc08541h\">https://doi.org/10.1039/c4cc08541h</a>.","ista":"Lee J-W, Klajn R. 2015. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. 51(11), 2036–2039.","ieee":"J.-W. Lee and R. Klajn, “Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2,” <i>Chemical Communications</i>, vol. 51, no. 11. Royal Society of Chemistry, pp. 2036–2039, 2015.","ama":"Lee J-W, Klajn R. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. <i>Chemical Communications</i>. 2015;51(11):2036-2039. doi:<a href=\"https://doi.org/10.1039/c4cc08541h\">10.1039/c4cc08541h</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/C4CC08541H"}],"quality_controlled":"1","author":[{"first_name":"Ji-Woong","last_name":"Lee","full_name":"Lee, Ji-Woong"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn"}],"extern":"1","abstract":[{"text":"Metallic nanoparticles co-functionalised with monolayers of UV- and CO2-sensitive ligands were prepared and shown to respond to these two types of stimuli reversibly and in an orthogonal fashion. The composition of the coating could be tailored to yield nanoparticles capable of aggregating exclusively when both UV and CO2 were applied at the same time, analogously to the behaviour of an AND logic gate.","lang":"eng"}],"publication_status":"published","pmid":1,"title":"Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2","publication":"Chemical Communications","_id":"13395","oa":1,"publisher":"Royal Society of Chemistry","article_type":"original","issue":"11","volume":51,"month":"11","date_created":"2023-08-01T09:44:48Z","status":"public","intvolume":"        51"},{"doi":"10.1021/la504291n","language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","date_updated":"2023-08-07T13:05:04Z","day":"27","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","publication_identifier":{"eissn":["1520-5827"],"issn":["0743-7463"]},"external_id":{"pmid":["25544061"]},"keyword":["Electrochemistry","Spectroscopy","Surfaces and Interfaces","Condensed Matter Physics","General Materials Science"],"date_published":"2015-01-27T00:00:00Z","page":"1048-1057","abstract":[{"text":"Photoswitching in densely packed azobenzene self-assembled monolayers (SAMs) is strongly affected by steric constraints and excitonic coupling between neighboring chromophores. Therefore, control of the chromophore density is essential for enhancing and manipulating the photoisomerization yield. We systematically compare two methods to achieve this goal: First, we assemble monocomponent azobenzene–alkanethiolate SAMs on gold nanoparticles of varying size. Second, we form mixed SAMs of azobenzene–alkanethiolates and “dummy” alkanethiolates on planar substrates. Both methods lead to a gradual decrease of the chromophore density and enable efficient photoswitching with low-power light sources. X-ray spectroscopy reveals that coadsorption from solution yields mixtures with tunable composition. The orientation of the chromophores with respect to the surface normal changes from a tilted to an upright position with increasing azobenzene density. For both systems, optical spectroscopy reveals a pronounced excitonic shift that increases with the chromophore density. In spite of exciting the optical transition of the monomer, the main spectral change in mixed SAMs occurs in the excitonic band. In addition, the photoisomerization yield decreases only slightly by increasing the azobenzene–alkanethiolate density, and we observed photoswitching even with minor dilutions. Unlike in solution, azobenzene in the planar SAM can be switched back almost completely by optical excitation from the cis to the original trans state within a short time scale. These observations indicate cooperativity in the photoswitching process of mixed SAMs.","lang":"eng"}],"publication_status":"published","pmid":1,"publication":"Langmuir","title":"Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature","_id":"13396","year":"2015","citation":{"mla":"Moldt, Thomas, et al. “Tailoring the Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface Curvature.” <i>Langmuir</i>, vol. 31, no. 3, American Chemical Society, 2015, pp. 1048–57, doi:<a href=\"https://doi.org/10.1021/la504291n\">10.1021/la504291n</a>.","apa":"Moldt, T., Brete, D., Przyrembel, D., Das, S., Goldman, J. R., Kundu, P. K., … Weinelt, M. (2015). Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. <i>Langmuir</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/la504291n\">https://doi.org/10.1021/la504291n</a>","short":"T. Moldt, D. Brete, D. Przyrembel, S. Das, J.R. Goldman, P.K. Kundu, C. Gahl, R. Klajn, M. Weinelt, Langmuir 31 (2015) 1048–1057.","chicago":"Moldt, Thomas, Daniel Brete, Daniel Przyrembel, Sanjib Das, Joel R. Goldman, Pintu K. Kundu, Cornelius Gahl, Rafal Klajn, and Martin Weinelt. “Tailoring the Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface Curvature.” <i>Langmuir</i>. American Chemical Society, 2015. <a href=\"https://doi.org/10.1021/la504291n\">https://doi.org/10.1021/la504291n</a>.","ista":"Moldt T, Brete D, Przyrembel D, Das S, Goldman JR, Kundu PK, Gahl C, Klajn R, Weinelt M. 2015. Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. 31(3), 1048–1057.","ama":"Moldt T, Brete D, Przyrembel D, et al. Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. <i>Langmuir</i>. 2015;31(3):1048-1057. doi:<a href=\"https://doi.org/10.1021/la504291n\">10.1021/la504291n</a>","ieee":"T. Moldt <i>et al.</i>, “Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature,” <i>Langmuir</i>, vol. 31, no. 3. American Chemical Society, pp. 1048–1057, 2015."},"extern":"1","author":[{"first_name":"Thomas","last_name":"Moldt","full_name":"Moldt, Thomas"},{"first_name":"Daniel","last_name":"Brete","full_name":"Brete, Daniel"},{"last_name":"Przyrembel","first_name":"Daniel","full_name":"Przyrembel, Daniel"},{"full_name":"Das, Sanjib","last_name":"Das","first_name":"Sanjib"},{"full_name":"Goldman, Joel R.","first_name":"Joel R.","last_name":"Goldman"},{"last_name":"Kundu","first_name":"Pintu K.","full_name":"Kundu, Pintu K."},{"first_name":"Cornelius","last_name":"Gahl","full_name":"Gahl, Cornelius"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal"},{"last_name":"Weinelt","first_name":"Martin","full_name":"Weinelt, Martin"}],"quality_controlled":"1","month":"01","date_created":"2023-08-01T09:45:02Z","status":"public","intvolume":"        31","publisher":"American Chemical Society","article_type":"original","volume":31,"issue":"3"},{"scopus_import":"1","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"keyword":["Physical and Theoretical Chemistry"],"external_id":{"pmid":["25920522"]},"date_published":"2015-01-02T00:00:00Z","page":"403-421","doi":"10.1039/c4fd00265b","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","oa_version":"Published Version","date_updated":"2023-08-07T13:06:23Z","type":"journal_article","day":"02","intvolume":"       181","month":"01","date_created":"2023-08-01T09:45:17Z","status":"public","volume":181,"publisher":"Royal Society of Chemistry","article_type":"original","pmid":1,"publication":"Faraday Discussions","title":"Magnetic field-induced self-assembly of iron oxide nanocubes","_id":"13397","oa":1,"abstract":[{"lang":"eng","text":"Self-assembly of inorganic nanoparticles has been studied extensively for particles having different sizes and compositions. However, relatively little attention has been devoted to how the shape and surface chemistry of magnetic nanoparticles affects their self-assembly properties. Here, we undertook a combined experiment–theory study aimed at better understanding of the self-assembly of cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental parameters, such as the direction of the magnetic field and nanoparticle density, a variety of superstructures can be obtained, including one-dimensional filaments and helices, as well as C-shaped assemblies described here for the first time. Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive ligands. Using these modified nanoparticles, we were able to achieve orthogonal control of self-assembly using a magnetic field and light."}],"publication_status":"published","citation":{"short":"G. Singh, H. Chan, T. Udayabhaskararao, E. Gelman, D. Peddis, A. Baskin, G. Leitus, P. Král, R. Klajn, Faraday Discussions 181 (2015) 403–421.","chicago":"Singh, Gurvinder, Henry Chan, T. Udayabhaskararao, Elijah Gelman, Davide Peddis, Artem Baskin, Gregory Leitus, Petr Král, and Rafal Klajn. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2015. <a href=\"https://doi.org/10.1039/c4fd00265b\">https://doi.org/10.1039/c4fd00265b</a>.","ista":"Singh G, Chan H, Udayabhaskararao T, Gelman E, Peddis D, Baskin A, Leitus G, Král P, Klajn R. 2015. Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. 181, 403–421.","ieee":"G. Singh <i>et al.</i>, “Magnetic field-induced self-assembly of iron oxide nanocubes,” <i>Faraday Discussions</i>, vol. 181. Royal Society of Chemistry, pp. 403–421, 2015.","ama":"Singh G, Chan H, Udayabhaskararao T, et al. Magnetic field-induced self-assembly of iron oxide nanocubes. <i>Faraday Discussions</i>. 2015;181:403-421. doi:<a href=\"https://doi.org/10.1039/c4fd00265b\">10.1039/c4fd00265b</a>","apa":"Singh, G., Chan, H., Udayabhaskararao, T., Gelman, E., Peddis, D., Baskin, A., … Klajn, R. (2015). Magnetic field-induced self-assembly of iron oxide nanocubes. <i>Faraday Discussions</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c4fd00265b\">https://doi.org/10.1039/c4fd00265b</a>","mla":"Singh, Gurvinder, et al. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” <i>Faraday Discussions</i>, vol. 181, Royal Society of Chemistry, 2015, pp. 403–21, doi:<a href=\"https://doi.org/10.1039/c4fd00265b\">10.1039/c4fd00265b</a>."},"main_file_link":[{"url":"https://doi.org/10.1039/C4FD00265B","open_access":"1"}],"author":[{"last_name":"Singh","first_name":"Gurvinder","full_name":"Singh, Gurvinder"},{"full_name":"Chan, Henry","first_name":"Henry","last_name":"Chan"},{"full_name":"Udayabhaskararao, T.","first_name":"T.","last_name":"Udayabhaskararao"},{"last_name":"Gelman","first_name":"Elijah","full_name":"Gelman, Elijah"},{"first_name":"Davide","last_name":"Peddis","full_name":"Peddis, Davide"},{"first_name":"Artem","last_name":"Baskin","full_name":"Baskin, Artem"},{"first_name":"Gregory","last_name":"Leitus","full_name":"Leitus, Gregory"},{"full_name":"Král, Petr","first_name":"Petr","last_name":"Král"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"}],"extern":"1","quality_controlled":"1","year":"2015"},{"volume":181,"article_type":"letter_note","publisher":"Royal Society of Chemistry","intvolume":"       181","date_created":"2023-08-01T09:45:29Z","month":"07","status":"public","citation":{"ama":"Sun Y, Scarabelli L, Kotov N, et al. Field-assisted self-assembly process: General discussion. <i>Faraday Discussions</i>. 2015;181:463-479. doi:<a href=\"https://doi.org/10.1039/c5fd90041g\">10.1039/c5fd90041g</a>","ieee":"Y. Sun <i>et al.</i>, “Field-assisted self-assembly process: General discussion,” <i>Faraday Discussions</i>, vol. 181. Royal Society of Chemistry, pp. 463–479, 2015.","short":"Y. Sun, L. Scarabelli, N. Kotov, M. Tebbe, X.-M. Lin, W. Brullot, L. Isa, P. Schurtenberger, H. Moehwald, I. Fedin, O. Velev, D. Faivre, C. Sorensen, R. Perzynski, M. Chanana, Z. Li, F. Bresme, P. Král, E. Firlar, D. Schiffrin, J.B. Souza Junior, A. Fery, E. Shevchenko, O. Tarhan, A.P. Alivisatos, S. Disch, R. Klajn, S. Ghosh, Faraday Discussions 181 (2015) 463–479.","chicago":"Sun, Yugang, Leonardo Scarabelli, Nicholas Kotov, Moritz Tebbe, Xiao-Min Lin, Ward Brullot, Lucio Isa, et al. “Field-Assisted Self-Assembly Process: General Discussion.” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2015. <a href=\"https://doi.org/10.1039/c5fd90041g\">https://doi.org/10.1039/c5fd90041g</a>.","ista":"Sun Y, Scarabelli L, Kotov N, Tebbe M, Lin X-M, Brullot W, Isa L, Schurtenberger P, Moehwald H, Fedin I, Velev O, Faivre D, Sorensen C, Perzynski R, Chanana M, Li Z, Bresme F, Král P, Firlar E, Schiffrin D, Souza Junior JB, Fery A, Shevchenko E, Tarhan O, Alivisatos AP, Disch S, Klajn R, Ghosh S. 2015. Field-assisted self-assembly process: General discussion. Faraday Discussions. 181, 463–479.","apa":"Sun, Y., Scarabelli, L., Kotov, N., Tebbe, M., Lin, X.-M., Brullot, W., … Ghosh, S. (2015). Field-assisted self-assembly process: General discussion. <i>Faraday Discussions</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c5fd90041g\">https://doi.org/10.1039/c5fd90041g</a>","mla":"Sun, Yugang, et al. “Field-Assisted Self-Assembly Process: General Discussion.” <i>Faraday Discussions</i>, vol. 181, Royal Society of Chemistry, 2015, pp. 463–79, doi:<a href=\"https://doi.org/10.1039/c5fd90041g\">10.1039/c5fd90041g</a>."},"quality_controlled":"1","extern":"1","author":[{"full_name":"Sun, Yugang","last_name":"Sun","first_name":"Yugang"},{"full_name":"Scarabelli, Leonardo","first_name":"Leonardo","last_name":"Scarabelli"},{"last_name":"Kotov","first_name":"Nicholas","full_name":"Kotov, Nicholas"},{"full_name":"Tebbe, Moritz","last_name":"Tebbe","first_name":"Moritz"},{"full_name":"Lin, Xiao-Min","last_name":"Lin","first_name":"Xiao-Min"},{"full_name":"Brullot, Ward","first_name":"Ward","last_name":"Brullot"},{"last_name":"Isa","first_name":"Lucio","full_name":"Isa, Lucio"},{"last_name":"Schurtenberger","first_name":"Peter","full_name":"Schurtenberger, Peter"},{"last_name":"Moehwald","first_name":"Helmuth","full_name":"Moehwald, Helmuth"},{"first_name":"Igor","last_name":"Fedin","full_name":"Fedin, Igor"},{"last_name":"Velev","first_name":"Orlin","full_name":"Velev, Orlin"},{"last_name":"Faivre","first_name":"Damien","full_name":"Faivre, Damien"},{"first_name":"Christopher","last_name":"Sorensen","full_name":"Sorensen, Christopher"},{"full_name":"Perzynski, Régine","first_name":"Régine","last_name":"Perzynski"},{"first_name":"Munish","last_name":"Chanana","full_name":"Chanana, Munish"},{"last_name":"Li","first_name":"Zhihai","full_name":"Li, Zhihai"},{"full_name":"Bresme, Fernando","last_name":"Bresme","first_name":"Fernando"},{"last_name":"Král","first_name":"Petr","full_name":"Král, Petr"},{"full_name":"Firlar, Emre","first_name":"Emre","last_name":"Firlar"},{"full_name":"Schiffrin, David","last_name":"Schiffrin","first_name":"David"},{"full_name":"Souza Junior, Joao Batista","first_name":"Joao Batista","last_name":"Souza Junior"},{"full_name":"Fery, Andreas","first_name":"Andreas","last_name":"Fery"},{"full_name":"Shevchenko, Elena","first_name":"Elena","last_name":"Shevchenko"},{"last_name":"Tarhan","first_name":"Ozgur","full_name":"Tarhan, Ozgur"},{"full_name":"Alivisatos, Armand Paul","last_name":"Alivisatos","first_name":"Armand Paul"},{"full_name":"Disch, Sabrina","last_name":"Disch","first_name":"Sabrina"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"},{"first_name":"Suvojit","last_name":"Ghosh","full_name":"Ghosh, Suvojit"}],"year":"2015","publication":"Faraday Discussions","title":"Field-assisted self-assembly process: General discussion","pmid":1,"_id":"13398","publication_status":"published","date_published":"2015-07-07T00:00:00Z","external_id":{"pmid":["26149295"]},"keyword":["Physical and Theoretical Chemistry"],"page":"463-479","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-08T07:16:20Z","oa_version":"None","day":"07","language":[{"iso":"eng"}],"doi":"10.1039/c5fd90041g"},{"citation":{"apa":"Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nplants.2015.94\">https://doi.org/10.1038/nplants.2015.94</a>","mla":"Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” <i>Nature Plants</i>, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/nplants.2015.94\">10.1038/nplants.2015.94</a>.","ieee":"L. Yu <i>et al.</i>, “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” <i>Nature Plants</i>, vol. 1, no. 7. Nature Publishing Group, 2015.","ama":"Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. <i>Nature Plants</i>. 2015;1(7). doi:<a href=\"https://doi.org/10.1038/nplants.2015.94\">10.1038/nplants.2015.94</a>","short":"L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015).","chicago":"Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nplants.2015.94\">https://doi.org/10.1038/nplants.2015.94</a>.","ista":"Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094."},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/"}],"author":[{"full_name":"Yu, Luo","last_name":"Yu","first_name":"Luo"},{"last_name":"Scholl","first_name":"Stefan","full_name":"Scholl, Stefan"},{"full_name":"Doering, Anett","last_name":"Doering","first_name":"Anett"},{"full_name":"Yi, Zhang","last_name":"Yi","first_name":"Zhang"},{"last_name":"Irani","first_name":"Niloufer","full_name":"Irani, Niloufer"},{"full_name":"Di Rubbo, Simone","first_name":"Simone","last_name":"Di Rubbo"},{"full_name":"Neumetzler, Lutz","first_name":"Lutz","last_name":"Neumetzler"},{"first_name":"Praveen","last_name":"Krishnamoorthy","full_name":"Krishnamoorthy, Praveen"},{"full_name":"Van Houtte, Isabelle","last_name":"Van Houtte","first_name":"Isabelle"},{"last_name":"Mylle","first_name":"Evelien","full_name":"Mylle, Evelien"},{"full_name":"Bischoff, Volker","last_name":"Bischoff","first_name":"Volker"},{"full_name":"Vernhettes, Samantha","last_name":"Vernhettes","first_name":"Samantha"},{"full_name":"Winne, Johan","last_name":"Winne","first_name":"Johan"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"York","last_name":"Stierhof","full_name":"Stierhof, York"},{"first_name":"Karin","last_name":"Schumacher","full_name":"Schumacher, Karin"},{"last_name":"Persson","first_name":"Staffan","full_name":"Persson, Staffan"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"quality_controlled":"1","year":"2015","publication":"Nature Plants","title":"V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis","pmid":1,"oa":1,"_id":"1383","publication_status":"published","abstract":[{"text":"In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants.","lang":"eng"}],"issue":"7","volume":1,"article_type":"original","publisher":"Nature Publishing Group","intvolume":"         1","publist_id":"5827","date_created":"2018-12-11T11:51:42Z","month":"07","status":"public","article_number":"15094","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_updated":"2021-01-12T06:50:18Z","oa_version":"Submitted Version","day":"06","language":[{"iso":"eng"}],"doi":"10.1038/nplants.2015.94","department":[{"_id":"JiFr"}],"date_published":"2015-07-06T00:00:00Z","external_id":{"pmid":["27250258"]},"scopus_import":1},{"_id":"1399","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"1662","status":"public","relation":"part_of_dissertation"},{"id":"1792","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"2255"}]},"title":"On the approximation of intrinsic volumes","abstract":[{"text":"This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold.","lang":"eng"}],"publication_status":"published","author":[{"first_name":"Florian","last_name":"Pausinger","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","citation":{"apa":"Pausinger, F. (2015). <i>On the approximation of intrinsic volumes</i>. Institute of Science and Technology Austria.","mla":"Pausinger, Florian. <i>On the Approximation of Intrinsic Volumes</i>. Institute of Science and Technology Austria, 2015.","ista":"Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","short":"F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science and Technology Austria, 2015.","chicago":"Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute of Science and Technology Austria, 2015.","ieee":"F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science and Technology Austria, 2015.","ama":"Pausinger F. On the approximation of intrinsic volumes. 2015."},"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert"}],"year":"2015","day":"01","oa_version":"None","date_updated":"2023-09-07T11:41:25Z","type":"dissertation","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"publist_id":"5808","alternative_title":["ISTA Thesis"],"status":"public","month":"06","date_created":"2018-12-11T11:51:48Z","page":"144","date_published":"2015-06-01T00:00:00Z","publisher":"Institute of Science and Technology Austria"}]