[{"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","day":"05","month":"05","language":[{"iso":"eng"}],"date_published":"2015-05-05T00:00:00Z","doi":"10.15479/AT:IST-2015-334-v1-1","page":"15","oa":1,"citation":{"ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit Distance for Pushdown Automata. IST Austria; 2015. doi:10.15479/AT:IST-2015-334-v1-1","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015). Edit distance for pushdown automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-334-v1-1","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, Edit distance for pushdown automata. IST Austria, 2015.","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for pushdown automata, IST Austria, 15p.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Edit Distance for Pushdown Automata, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. Edit Distance for Pushdown Automata. IST Austria, 2015, doi:10.15479/AT:IST-2015-334-v1-1.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. Edit Distance for Pushdown Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-334-v1-1."},"abstract":[{"lang":"eng","text":"The edit distance between two words w1, w2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w1 to w2. The edit distance generalizes to languages L1, L2, where the edit distance is the minimal number k such that for every word from L1 there exists a word in L2 with edit distance at most k. We study the edit distance computation problem between pushdown automata and their subclasses.\r\nThe problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for deciding whether, for a given threshold k, the edit distance from a pushdown automaton to a finite automaton is at most k. "}],"file_date_updated":"2020-07-14T12:46:55Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report","file":[{"file_size":422573,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2015-334-v1+1_report.pdf","checksum":"8a5f2d77560e552af87eb1982437a43b","date_created":"2018-12-12T11:53:56Z","date_updated":"2020-07-14T12:46:55Z","relation":"main_file","file_id":"5518"}],"oa_version":"Published Version","date_created":"2018-12-12T11:39:20Z","date_updated":"2023-02-23T12:20:08Z","related_material":{"record":[{"id":"1610","status":"public","relation":"later_version"},{"relation":"later_version","status":"public","id":"465"}]},"pubrep_id":"334","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop"}],"department":[{"_id":"KrCh"}],"publisher":"IST Austria","status":"public","title":"Edit distance for pushdown automata","ddc":["004"],"publication_status":"published","_id":"5438","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"published","title":"The complexity of evolutionary games on graphs","status":"public","ddc":["005","576"],"department":[{"_id":"KrCh"}],"publisher":"IST Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5440","year":"2015","date_created":"2018-12-12T11:39:21Z","date_updated":"2023-02-23T12:26:10Z","oa_version":"Published Version","file":[{"checksum":"66aace7d367032af97c15e35c9be9636","date_updated":"2020-07-14T12:46:56Z","date_created":"2018-12-12T11:53:23Z","relation":"main_file","file_id":"5484","content_type":"application/pdf","file_size":466161,"creator":"system","access_level":"open_access","file_name":"IST-2015-323-v2+2_main.pdf"}],"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"related_material":{"record":[{"id":"5421","relation":"earlier_version","status":"public"},{"relation":"earlier_version","status":"public","id":"5432"}]},"pubrep_id":"338","alternative_title":["IST Austria Technical Report"],"type":"technical_report","file_date_updated":"2020-07-14T12:46:56Z","abstract":[{"text":"Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom for payoff in the context of evolution. The replacement graph specifies who competes with whom for reproduction. The vertices of the two graphs are the same, and each vertex corresponds to an individual of the population. The fitness (or the reproductive rate) is a non-negative number, and depends on the payoff. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. Our main results are as follows: First, we consider a special case of the general problem, where the residents do not reproduce. We show that the qualitative question is NP-complete, and the quantitative approximation question is #P-complete, and the hardness results hold even in the special case where the interaction and the replacement graphs coincide. Second, we show that in general both the qualitative and the quantitative approximation questions are PSPACE-complete. The PSPACE-hardness result for quantitative approximation holds even when the fitness is always positive.","lang":"eng"}],"page":"18","citation":{"apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v2-2","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary games on graphs. IST Austria, 2015.","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 18p.","ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolutionary Games on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v2-2","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v2-2.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary Games on Graphs, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v2-2."},"oa":1,"language":[{"iso":"eng"}],"date_published":"2015-06-16T00:00:00Z","doi":"10.15479/AT:IST-2015-323-v2-2","month":"06","day":"16","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]}},{"page":"29","citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolutionary Games on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v1-1","apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v1-1","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary games on graphs. IST Austria, 2015.","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 29p.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary Games on Graphs, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v1-1.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v1-1."},"oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2015-323-v1-1","date_published":"2015-02-19T00:00:00Z","day":"19","month":"02","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","title":"The complexity of evolutionary games on graphs","ddc":["005","576"],"status":"public","publisher":"IST Austria","department":[{"_id":"KrCh"}],"_id":"5432","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","date_updated":"2023-02-23T12:26:33Z","date_created":"2018-12-12T11:39:18Z","file":[{"file_id":"5519","relation":"main_file","checksum":"546c1b291d545e7b24aaaf4199dac671","date_updated":"2020-07-14T12:46:53Z","date_created":"2018-12-12T11:53:57Z","access_level":"open_access","file_name":"IST-2015-323-v1+1_main.pdf","creator":"system","content_type":"application/pdf","file_size":576347}],"oa_version":"Published Version","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5421"},{"id":"5440","status":"public","relation":"later_version"}]},"pubrep_id":"323","alternative_title":["IST Austria Technical Report"],"type":"technical_report","abstract":[{"lang":"eng","text":"Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom in the context of evolution.The replacement graph specifies who competes with whom for reproduction. \r\nThe vertices of the two graphs are the same, and each vertex corresponds to an individual of the population. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. \r\nOur main results are:\r\n(1) We show that the qualitative question is NP-complete and the quantitative approximation question is #P-hard in the special case when the interaction and the replacement graphs coincide and even with the restriction that the resident individuals do not reproduce (which corresponds to an invading population taking over an empty structure).\r\n(2) We show that in general the qualitative question is PSPACE-complete and the quantitative approximation question is PSPACE-hard and can be solved in exponential time.\r\n"}],"file_date_updated":"2020-07-14T12:46:53Z"},{"page":"25","oa":1,"citation":{"ista":"Reiter J, Makohon-Moore A, Gerold J, Bozic I, Chatterjee K, Iacobuzio-Donahue C, Vogelstein B, Nowak M. 2015. Reconstructing robust phylogenies of metastatic cancers, IST Austria, 25p.","apa":"Reiter, J., Makohon-Moore, A., Gerold, J., Bozic, I., Chatterjee, K., Iacobuzio-Donahue, C., … Nowak, M. (2015). Reconstructing robust phylogenies of metastatic cancers. IST Austria. https://doi.org/10.15479/AT:IST-2015-399-v1-1","ieee":"J. Reiter et al., Reconstructing robust phylogenies of metastatic cancers. IST Austria, 2015.","ama":"Reiter J, Makohon-Moore A, Gerold J, et al. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria; 2015. doi:10.15479/AT:IST-2015-399-v1-1","chicago":"Reiter, Johannes, Alvin Makohon-Moore, Jeffrey Gerold, Ivana Bozic, Krishnendu Chatterjee, Christine Iacobuzio-Donahue, Bert Vogelstein, and Martin Nowak. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-399-v1-1.","mla":"Reiter, Johannes, et al. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria, 2015, doi:10.15479/AT:IST-2015-399-v1-1.","short":"J. Reiter, A. Makohon-Moore, J. Gerold, I. Bozic, K. Chatterjee, C. Iacobuzio-Donahue, B. Vogelstein, M. Nowak, Reconstructing Robust Phylogenies of Metastatic Cancers, IST Austria, 2015."},"language":[{"iso":"eng"}],"date_published":"2015-12-30T00:00:00Z","doi":"10.15479/AT:IST-2015-399-v1-1","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","month":"12","day":"30","department":[{"_id":"KrCh"}],"publisher":"IST Austria","publication_status":"published","ddc":["000","576"],"title":"Reconstructing robust phylogenies of metastatic cancers","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5444","year":"2015","oa_version":"Published Version","file":[{"checksum":"c47d33bdda06181753c0af36f16e7b5d","date_created":"2018-12-12T11:53:24Z","date_updated":"2020-07-14T12:46:58Z","relation":"main_file","file_id":"5485","content_type":"application/pdf","file_size":3533200,"creator":"system","access_level":"open_access","file_name":"IST-2015-399-v1+1_treeomics.pdf"}],"date_created":"2018-12-12T11:39:22Z","date_updated":"2020-07-14T23:05:07Z","pubrep_id":"399","author":[{"full_name":"Reiter, Johannes","first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353"},{"last_name":"Makohon-Moore","first_name":"Alvin","full_name":"Makohon-Moore, Alvin"},{"last_name":"Gerold","first_name":"Jeffrey","full_name":"Gerold, Jeffrey"},{"full_name":"Bozic, Ivana","last_name":"Bozic","first_name":"Ivana"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Iacobuzio-Donahue, Christine","first_name":"Christine","last_name":"Iacobuzio-Donahue"},{"first_name":"Bert","last_name":"Vogelstein","full_name":"Vogelstein, Bert"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","abstract":[{"lang":"eng","text":"A comprehensive understanding of the clonal evolution of cancer is critical for understanding neoplasia. Genome-wide sequencing data enables evolutionary studies at unprecedented depth. However, classical phylogenetic methods often struggle with noisy sequencing data of impure DNA samples and fail to detect subclones that have different evolutionary trajectories. We have developed a tool, called Treeomics, that allows us to reconstruct the phylogeny of a cancer with commonly available sequencing technologies. Using Bayesian inference and Integer Linear Programming, robust phylogenies consistent with the biological processes underlying cancer evolution were obtained for pancreatic, ovarian, and prostate cancers. Furthermore, Treeomics correctly identified sequencing artifacts such as those resulting from low statistical power; nearly 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumor heterogeneity among distinct samples. Importantly, we show that the evolutionary trees generated with Treeomics are mathematically optimal."}],"file_date_updated":"2020-07-14T12:46:58Z"},{"month":"11","day":"06","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"oa":1,"citation":{"chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-325-v2-1.","short":"K. Chatterjee, M. Chmelik, J. Davies, A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs. IST Austria, 2015, doi:10.15479/AT:IST-2015-325-v2-1.","ieee":"K. Chatterjee, M. Chmelik, and J. Davies, A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs. IST Austria, 2015.","apa":"Chatterjee, K., Chmelik, M., & Davies, J. (2015). A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs. IST Austria. https://doi.org/10.15479/AT:IST-2015-325-v2-1","ista":"Chatterjee K, Chmelik M, Davies J. 2015. A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs, IST Austria, 23p.","ama":"Chatterjee K, Chmelik M, Davies J. A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs. IST Austria; 2015. doi:10.15479/AT:IST-2015-325-v2-1"},"page":"23","date_published":"2015-11-06T00:00:00Z","doi":"10.15479/AT:IST-2015-325-v2-1","language":[{"iso":"eng"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"abstract":[{"text":"POMDPs are standard models for probabilistic planning problems, where an agent interacts with an uncertain environment. We study the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a policy to ensure that the target set is reached with probability 1 (almost-surely). While in general the problem is EXPTIME-complete, in many practical cases policies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. In this work, we first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:57Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5443","year":"2015","ddc":["000"],"status":"public","title":"A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs","publication_status":"published","publisher":"IST Austria","department":[{"_id":"KrCh"}],"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","first_name":"Martin"},{"full_name":"Davies, Jessica","id":"378E0060-F248-11E8-B48F-1D18A9856A87","last_name":"Davies","first_name":"Jessica"}],"related_material":{"record":[{"id":"1166","relation":"later_version","status":"public"}]},"pubrep_id":"362","date_created":"2018-12-12T11:39:22Z","date_updated":"2023-02-21T16:24:05Z","file":[{"creator":"system","file_size":412379,"content_type":"application/pdf","file_name":"IST-2015-325-v2+1_main.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:57Z","date_created":"2018-12-12T11:53:05Z","checksum":"f0fa31ad8161ed655137e94012123ef9","file_id":"5466","relation":"main_file"}],"oa_version":"Published Version"},{"author":[{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","last_name":"Biswas"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"}],"oa_version":"None","volume":624,"date_created":"2019-01-08T20:44:06Z","date_updated":"2021-01-12T08:03:36Z","_id":"5804","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 624","publisher":"Elsevier","title":"From prima quadraginta octant to lattice sphere through primitive integer operations","publication_status":"published","status":"public","issue":"4","abstract":[{"lang":"eng","text":"We present here the first integer-based algorithm for constructing a well-defined lattice sphere specified by integer radius and integer center. The algorithm evolves from a unique correspondence between the lattice points comprising the sphere and the distribution of sum of three square numbers in integer intervals. We characterize these intervals to derive a useful set of recurrences, which, in turn, aids in efficient computation. Each point of the lattice sphere is determined by resorting to only a few primitive operations in the integer domain. The symmetry of its quadraginta octants provides an added advantage by confining the computation to its prima quadraginta octant. Detailed theoretical analysis and experimental results have been furnished to demonstrate its simplicity and elegance."}],"extern":"1","type":"journal_article","doi":"10.1016/j.tcs.2015.11.018","date_published":"2015-04-18T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Biswas R, Bhowmick P. From prima quadraginta octant to lattice sphere through primitive integer operations. Theoretical Computer Science. 2015;624(4):56-72. doi:10.1016/j.tcs.2015.11.018","ista":"Biswas R, Bhowmick P. 2015. From prima quadraginta octant to lattice sphere through primitive integer operations. Theoretical Computer Science. 624(4), 56–72.","ieee":"R. Biswas and P. Bhowmick, “From prima quadraginta octant to lattice sphere through primitive integer operations,” Theoretical Computer Science, vol. 624, no. 4. Elsevier, pp. 56–72, 2015.","apa":"Biswas, R., & Bhowmick, P. (2015). From prima quadraginta octant to lattice sphere through primitive integer operations. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.11.018","mla":"Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to Lattice Sphere through Primitive Integer Operations.” Theoretical Computer Science, vol. 624, no. 4, Elsevier, 2015, pp. 56–72, doi:10.1016/j.tcs.2015.11.018.","short":"R. Biswas, P. Bhowmick, Theoretical Computer Science 624 (2015) 56–72.","chicago":"Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to Lattice Sphere through Primitive Integer Operations.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.11.018."},"publication":"Theoretical Computer Science","page":"56-72","quality_controlled":"1","publication_identifier":{"issn":["0304-3975"]},"day":"18","month":"04"},{"month":"11","day":"09","publication_identifier":{"issn":["0304-3975"]},"quality_controlled":"1","page":"146-163","publication":"Theoretical Computer Science","citation":{"short":"R. Biswas, P. Bhowmick, Theoretical Computer Science 605 (2015) 146–163.","mla":"Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical Geodesic Paths and Circles InZ3.” Theoretical Computer Science, vol. 605, no. 11, Elsevier, 2015, pp. 146–63, doi:10.1016/j.tcs.2015.09.003.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical Geodesic Paths and Circles InZ3.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.09.003.","ama":"Biswas R, Bhowmick P. On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. 2015;605(11):146-163. doi:10.1016/j.tcs.2015.09.003","ieee":"R. Biswas and P. Bhowmick, “On different topological classes of spherical geodesic paths and circles inZ3,” Theoretical Computer Science, vol. 605, no. 11. Elsevier, pp. 146–163, 2015.","apa":"Biswas, R., & Bhowmick, P. (2015). On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.09.003","ista":"Biswas R, Bhowmick P. 2015. On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. 605(11), 146–163."},"language":[{"iso":"eng"}],"date_published":"2015-11-09T00:00:00Z","doi":"10.1016/j.tcs.2015.09.003","type":"journal_article","extern":"1","issue":"11","status":"public","title":"On different topological classes of spherical geodesic paths and circles inZ3","publication_status":"published","intvolume":" 605","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5807","year":"2015","date_created":"2019-01-08T20:44:52Z","date_updated":"2021-01-12T08:03:37Z","volume":605,"oa_version":"None","author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","last_name":"Biswas","full_name":"Biswas, Ranita"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"}]},{"type":"journal_article","extern":"1","issue":"6-8","publisher":"Springer Nature","intvolume":" 31","publication_status":"published","status":"public","title":"Layer the sphere","year":"2015","_id":"5808","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":31,"oa_version":"None","date_created":"2019-01-08T20:45:05Z","date_updated":"2021-01-12T08:03:37Z","author":[{"full_name":"Biswas, Ranita","last_name":"Biswas","first_name":"Ranita","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"publication_identifier":{"issn":["0178-2789","1432-2315"]},"month":"05","day":"08","page":"787-797","quality_controlled":"1","citation":{"short":"R. Biswas, P. Bhowmick, The Visual Computer 31 (2015) 787–797.","mla":"Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual Computer, vol. 31, no. 6–8, Springer Nature, 2015, pp. 787–97, doi:10.1007/s00371-015-1101-3.","chicago":"Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual Computer. Springer Nature, 2015. https://doi.org/10.1007/s00371-015-1101-3.","ama":"Biswas R, Bhowmick P. Layer the sphere. The Visual Computer. 2015;31(6-8):787-797. doi:10.1007/s00371-015-1101-3","ieee":"R. Biswas and P. Bhowmick, “Layer the sphere,” The Visual Computer, vol. 31, no. 6–8. Springer Nature, pp. 787–797, 2015.","apa":"Biswas, R., & Bhowmick, P. (2015). Layer the sphere. The Visual Computer. Springer Nature. https://doi.org/10.1007/s00371-015-1101-3","ista":"Biswas R, Bhowmick P. 2015. Layer the sphere. The Visual Computer. 31(6–8), 787–797."},"publication":"The Visual Computer","language":[{"iso":"eng"}],"doi":"10.1007/s00371-015-1101-3","date_published":"2015-05-08T00:00:00Z"},{"author":[{"first_name":"Sarah","last_name":"Sainsbury","full_name":"Sainsbury, Sarah"},{"full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","first_name":"Carrie A","last_name":"Bernecky"},{"full_name":"Cramer, Patrick","last_name":"Cramer","first_name":"Patrick"}],"date_updated":"2021-01-12T08:05:16Z","date_created":"2018-12-11T11:47:23Z","oa_version":"None","volume":16,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"594","year":"2015","status":"public","publication_status":"published","title":"Structural basis of transcription initiation by RNA polymerase II","publisher":"Nature Publishing Group","intvolume":" 16","abstract":[{"text":"Transcription of eukaryotic protein-coding genes commences with the assembly of a conserved initiation complex, which consists of RNA polymerase II (Pol II) and the general transcription factors, at promoter DNA. After two decades of research, the structural basis of transcription initiation is emerging. Crystal structures of many components of the initiation complex have been resolved, and structural information on Pol II complexes with general transcription factors has recently been obtained. Although mechanistic details await elucidation, available data outline how Pol II cooperates with the general transcription factors to bind to and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the promoter.","lang":"eng"}],"publist_id":"7206","issue":"3","extern":"1","type":"journal_article","doi":"10.1038/nrm3952","date_published":"2015-03-26T00:00:00Z","language":[{"iso":"eng"}],"publication":"Nature Reviews Molecular Cell Biology","citation":{"ama":"Sainsbury S, Bernecky C, Cramer P. Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 2015;16(3):129-143. doi:10.1038/nrm3952","apa":"Sainsbury, S., Bernecky, C., & Cramer, P. (2015). Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. Nature Publishing Group. https://doi.org/10.1038/nrm3952","ieee":"S. Sainsbury, C. Bernecky, and P. Cramer, “Structural basis of transcription initiation by RNA polymerase II,” Nature Reviews Molecular Cell Biology, vol. 16, no. 3. Nature Publishing Group, pp. 129–143, 2015.","ista":"Sainsbury S, Bernecky C, Cramer P. 2015. Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 16(3), 129–143.","short":"S. Sainsbury, C. Bernecky, P. Cramer, Nature Reviews Molecular Cell Biology 16 (2015) 129–143.","mla":"Sainsbury, Sarah, et al. “Structural Basis of Transcription Initiation by RNA Polymerase II.” Nature Reviews Molecular Cell Biology, vol. 16, no. 3, Nature Publishing Group, 2015, pp. 129–43, doi:10.1038/nrm3952.","chicago":"Sainsbury, Sarah, Carrie Bernecky, and Patrick Cramer. “Structural Basis of Transcription Initiation by RNA Polymerase II.” Nature Reviews Molecular Cell Biology. Nature Publishing Group, 2015. https://doi.org/10.1038/nrm3952."},"page":"129 - 143","day":"26","month":"03","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SOCG.2015.476","conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Eindhoven, Netherlands","start_date":"2015-06-22","end_date":"2015-06-25"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"06","volume":"34 ","date_updated":"2023-02-23T12:38:00Z","date_created":"2018-12-11T11:52:27Z","related_material":{"record":[{"id":"610","status":"public","relation":"later_version"}]},"author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"last_name":"Mabillard","first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac"},{"full_name":"Paták, Pavel","last_name":"Paták","first_name":"Pavel"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","first_name":"Zuzana"},{"full_name":"Tancer, Martin","first_name":"Martin","last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1191-6714"},{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2015","acknowledgement":"The work by Z. P. was partially supported by the Charles University Grant SVV-2014-260103. The\r\nwork by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of\r\nthe Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research\r\nwork of M. T. was conducted at IST Austria, supported by an IST Fellowship. The work by U.W.\r\nwas partially supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and\r\nSNSF-PP00P2-138948).","publist_id":"5666","ec_funded":1,"file_date_updated":"2020-07-14T12:44:59Z","date_published":"2015-06-11T00:00:00Z","page":"476 - 490","citation":{"ama":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:476-490. doi:10.4230/LIPIcs.SOCG.2015.476","ista":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2015. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 476–490.","apa":"Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2015). On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result (Vol. 34, pp. 476–490). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.476","ieee":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 476–490.","mla":"Goaoc, Xavier, et al. On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–90, doi:10.4230/LIPIcs.SOCG.2015.476.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–490.","chicago":"Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result,” 34:476–90. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.476."},"has_accepted_license":"1","day":"11","scopus_import":1,"file":[{"file_id":"4871","relation":"main_file","date_created":"2018-12-12T10:11:18Z","date_updated":"2020-07-14T12:44:59Z","checksum":"0945811875351796324189312ca29e9e","file_name":"IST-2016-502-v1+1_42.pdf","access_level":"open_access","creator":"system","file_size":636735,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"502","status":"public","title":"On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1511","abstract":[{"text":"The fact that the complete graph K_5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph K_n embeds in a closed surface M if and only if (n-3)(n-4) is at most 6b_1(M), where b_1(M) is the first Z_2-Betti number of M. On the other hand, Van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of K_{n+1}) embeds in R^{2k} if and only if n is less or equal to 2k+2. Two decades ago, Kuhnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k-1)-connected 2k-manifold with kth Z_2-Betti number b_k only if the following generalized Heawood inequality holds: binom{n-k-1}{k+1} is at most binom{2k+1}{k+1} b_k. This is a common generalization of the case of graphs on surfaces as well as the Van Kampen--Flores theorem. In the spirit of Kuhnel's conjecture, we prove that if the k-skeleton of the n-simplex embeds in a 2k-manifold with kth Z_2-Betti number b_k, then n is at most 2b_k binom{2k+2}{k} + 2k + 5. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k-1)-connected. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference"},{"day":"07","has_accepted_license":"1","page":"E3525-E3534","publication":"Proceedings of the National Academy of Sciences","citation":{"short":"L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 112 (2015) E3525–E3534.","mla":"Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” Proceedings of the National Academy of Sciences, vol. 112, no. 27, National Academy of Sciences, 2015, pp. E3525–34, doi:10.1073/pnas.1423808112.","chicago":"Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423808112.","ama":"Fenk LA, de Bono M. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. 2015;112(27):E3525-E3534. doi:10.1073/pnas.1423808112","apa":"Fenk, L. A., & de Bono, M. (2015). Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1423808112","ieee":"L. A. Fenk and M. de Bono, “Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity,” Proceedings of the National Academy of Sciences, vol. 112, no. 27. National Academy of Sciences, pp. E3525–E3534, 2015.","ista":"Fenk LA, de Bono M. 2015. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. 112(27), E3525–E3534."},"date_published":"2015-07-07T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Carbon dioxide (CO2) gradients are ubiquitous and provide animals with information about their environment, such as the potential presence of prey or predators. The nematode Caenorhabditis elegans avoids elevated CO2, and previous work identified three neuron pairs called “BAG,” “AFD,” and “ASE” that respond to CO2 stimuli. Using in vivo Ca2+ imaging and behavioral analysis, we show that C. elegans can detect CO2 independently of these sensory pathways. Many of the C. elegans sensory neurons we examined, including the AWC olfactory neurons, the ASJ and ASK gustatory neurons, and the ASH and ADL nociceptors, respond to a rise in CO2 with a rise in Ca2+. In contrast, glial sheath cells harboring the sensory endings of C. elegans’ major chemosensory neurons exhibit strong and sustained decreases in Ca2+ in response to high CO2. Some of these CO2 responses appear to be cell intrinsic. Worms therefore may couple detection of CO2 to that of other cues at the earliest stages of sensory processing. We show that C. elegans persistently suppresses oviposition at high CO2. Hermaphrodite-specific neurons (HSNs), the executive neurons driving egg-laying, are tonically inhibited when CO2 is elevated. CO2 modulates the egg-laying system partly through the AWC olfactory neurons: High CO2 tonically activates AWC by a cGMP-dependent mechanism, and AWC output inhibits the HSNs. Our work shows that CO2 is a more complex sensory cue for C. elegans than previously thought, both in terms of behavior and neural circuitry."}],"issue":"27","ddc":["570"],"title":"Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity","status":"public","intvolume":" 112","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6118","oa_version":"Published Version","file":[{"file_name":"2015_PNAS_Fenk.pdf","access_level":"open_access","file_size":2822681,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"6119","date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-19T14:21:07Z","checksum":"3d2da5af8d72467e382a565abc2e003d"}],"month":"07","publication_identifier":{"issn":["0027-8424","1091-6490"]},"quality_controlled":"1","oa":1,"external_id":{"pmid":["26100886"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1423808112","extern":"1","file_date_updated":"2020-07-14T12:47:20Z","publication_status":"published","publisher":"National Academy of Sciences","year":"2015","pmid":1,"date_created":"2019-03-19T14:15:50Z","date_updated":"2021-01-12T08:06:12Z","volume":112,"author":[{"first_name":"Lorenz A.","last_name":"Fenk","full_name":"Fenk, Lorenz A."},{"full_name":"de Bono, Mario","first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443"}]},{"publication":"eLife","citation":{"apa":"Laurent, P., Soltesz, Z., Nelson, G. M., Chen, C., Arellano-Carbajal, F., Levy, E., & de Bono, M. (2015). Decoding a neural circuit controlling global animal state in C. elegans. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.04241","ieee":"P. Laurent et al., “Decoding a neural circuit controlling global animal state in C. elegans,” eLife, vol. 4. eLife Sciences Publications, 2015.","ista":"Laurent P, Soltesz Z, Nelson GM, Chen C, Arellano-Carbajal F, Levy E, de Bono M. 2015. Decoding a neural circuit controlling global animal state in C. elegans. eLife. 4, e04241.","ama":"Laurent P, Soltesz Z, Nelson GM, et al. Decoding a neural circuit controlling global animal state in C. elegans. eLife. 2015;4. doi:10.7554/elife.04241","chicago":"Laurent, Patrick, Zoltan Soltesz, Geoffrey M Nelson, Changchun Chen, Fausto Arellano-Carbajal, Emmanuel Levy, and Mario de Bono. “Decoding a Neural Circuit Controlling Global Animal State in C. Elegans.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/elife.04241.","short":"P. Laurent, Z. Soltesz, G.M. Nelson, C. Chen, F. Arellano-Carbajal, E. Levy, M. de Bono, ELife 4 (2015).","mla":"Laurent, Patrick, et al. “Decoding a Neural Circuit Controlling Global Animal State in C. Elegans.” ELife, vol. 4, e04241, eLife Sciences Publications, 2015, doi:10.7554/elife.04241."},"date_published":"2015-03-11T00:00:00Z","day":"11","has_accepted_license":"1","ddc":["570"],"status":"public","title":"Decoding a neural circuit controlling global animal state in C. elegans","intvolume":" 4","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6120","oa_version":"Published Version","file":[{"creator":"kschuh","content_type":"application/pdf","file_size":6723528,"access_level":"open_access","file_name":"2015_elife_Laurent.pdf","checksum":"cf641b7a363aecd0a101755d23dee7e0","date_created":"2019-03-19T14:29:43Z","date_updated":"2020-07-14T12:47:20Z","file_id":"6121","relation":"main_file"}],"type":"journal_article","abstract":[{"text":"Brains organize behavior and physiology to optimize the response to threats or opportunities. We dissect how 21% O2, an indicator of surface exposure, reprograms C. elegans' global state, inducing sustained locomotory arousal and altering expression of neuropeptides, metabolic enzymes, and other non-neural genes. The URX O2-sensing neurons drive arousal at 21% O2 by tonically activating the RMG interneurons. Stimulating RMG is sufficient to switch behavioral state. Ablating the ASH, ADL, or ASK sensory neurons connected to RMG by gap junctions does not disrupt arousal. However, disrupting cation currents in these neurons curtails RMG neurosecretion and arousal. RMG signals high O2 by peptidergic secretion. Neuropeptide reporters reveal neural circuit state, as neurosecretion stimulates neuropeptide expression. Neural imaging in unrestrained animals shows that URX and RMG encode O2 concentration rather than behavior, while the activity of downstream interneurons such as AVB and AIY reflect both O2 levels and the behavior being executed.","lang":"eng"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["25760081"]},"language":[{"iso":"eng"}],"doi":"10.7554/elife.04241","month":"03","publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","publisher":"eLife Sciences Publications","year":"2015","pmid":1,"date_updated":"2021-01-12T08:06:13Z","date_created":"2019-03-19T14:23:51Z","volume":4,"author":[{"first_name":"Patrick","last_name":"Laurent","full_name":"Laurent, Patrick"},{"full_name":"Soltesz, Zoltan","last_name":"Soltesz","first_name":"Zoltan"},{"full_name":"Nelson, Geoffrey M","first_name":"Geoffrey M","last_name":"Nelson"},{"full_name":"Chen, Changchun","first_name":"Changchun","last_name":"Chen"},{"full_name":"Arellano-Carbajal, Fausto","last_name":"Arellano-Carbajal","first_name":"Fausto"},{"first_name":"Emmanuel","last_name":"Levy","full_name":"Levy, Emmanuel"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario","full_name":"de Bono, Mario"}],"article_number":"e04241","extern":"1","file_date_updated":"2020-07-14T12:47:20Z"},{"abstract":[{"lang":"eng","text":"An instance of the Valued Constraint Satisfaction Problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P ≠ NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in {0, ∞} corresponds to ordinary CSPs, where one deals only with the feasibility issue and there is no optimization. This case is the subject of the Algebraic CSP Dichotomy Conjecture predicting for which constraint languages CSPs are tractable (i.e. solvable in polynomial time) and for which NP-hard. The case when all allowed functions take only finite values corresponds to finite-valued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Zivny. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e. the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs."}],"type":"conference","alternative_title":["56th Annual Symposium on Foundations of Computer Science"],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1637","title":"The complexity of general-valued CSPs","status":"public","day":"01","scopus_import":1,"date_published":"2015-12-01T00:00:00Z","citation":{"ama":"Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. In: IEEE; 2015:1246-1258. doi:10.1109/FOCS.2015.80","ista":"Kolmogorov V, Krokhin A, Rolinek M. 2015. The complexity of general-valued CSPs. FOCS: Foundations of Computer Science, 56th Annual Symposium on Foundations of Computer Science, , 1246–1258.","apa":"Kolmogorov, V., Krokhin, A., & Rolinek, M. (2015). The complexity of general-valued CSPs (pp. 1246–1258). Presented at the FOCS: Foundations of Computer Science, Berkeley, CA, United States: IEEE. https://doi.org/10.1109/FOCS.2015.80","ieee":"V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued CSPs,” presented at the FOCS: Foundations of Computer Science, Berkeley, CA, United States, 2015, pp. 1246–1258.","mla":"Kolmogorov, Vladimir, et al. The Complexity of General-Valued CSPs. IEEE, 2015, pp. 1246–58, doi:10.1109/FOCS.2015.80.","short":"V. Kolmogorov, A. Krokhin, M. Rolinek, in:, IEEE, 2015, pp. 1246–1258.","chicago":"Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity of General-Valued CSPs,” 1246–58. IEEE, 2015. https://doi.org/10.1109/FOCS.2015.80."},"page":"1246 - 1258","ec_funded":1,"publist_id":"5518","related_material":{"record":[{"id":"644","relation":"other","status":"public"}]},"author":[{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"full_name":"Krokhin, Andrei","first_name":"Andrei","last_name":"Krokhin"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","last_name":"Rolinek","first_name":"Michal","full_name":"Rolinek, Michal"}],"date_updated":"2023-02-23T12:44:26Z","date_created":"2018-12-11T11:53:10Z","year":"2015","department":[{"_id":"VlKo"}],"publisher":"IEEE","publication_status":"published","month":"12","doi":"10.1109/FOCS.2015.80","conference":{"name":"FOCS: Foundations of Computer Science","start_date":"2015-10-18","location":"Berkeley, CA, United States","end_date":"2015-10-20"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.07327"}],"project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"quality_controlled":"1"},{"extern":"1","issue":"5","abstract":[{"text":"The osteoclast-associated receptor (OSCAR) is a collagen-binding immune receptor with important roles in dendritic cell maturation and activation of inflammatory monocytes as well as in osteoclastogenesis. The crystal structure of the OSCAR ectodomain is presented, both free and in complex with a consensus triple-helical peptide (THP). The structures revealed a collagen-binding site in each immunoglobulin-like domain (D1 and D2). The THP binds near a predicted collagen-binding groove in D1, but a more extensive interaction with D2 is facilitated by the unusually wide D1-D2 interdomain angle in OSCAR. Direct binding assays, combined with site-directed mutagenesis, confirm that the primary collagen-binding site in OSCAR resides in D2, in marked contrast to the related collagen receptors, glycoprotein VI (GPVI) and leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1). Monomeric OSCAR D1D2 binds to the consensus THP with a KD of 28 µM measured in solution, but shows a higher affinity (KD 1.5 μM) when binding to a solid-phase THP, most likely due to an avidity effect. These data suggest a 2-stage model for the interaction of OSCAR with a collagen fibril, with transient, low-affinity interactions initiated by the membrane-distal D1, followed by firm adhesion to the primary binding site in D2.","lang":"eng"}],"type":"journal_article","volume":127,"oa_version":"None","date_created":"2019-05-31T09:38:50Z","date_updated":"2021-01-12T08:07:47Z","author":[{"orcid":"0000-0002-1864-8951","id":"3E751364-F248-11E8-B48F-1D18A9856A87","last_name":"Zhou","first_name":"Long","full_name":"Zhou, Long"},{"first_name":"J. M.","last_name":"Hinerman","full_name":"Hinerman, J. M."},{"full_name":"Blaszczyk, M.","last_name":"Blaszczyk","first_name":"M."},{"full_name":"Miller, J. L. C.","first_name":"J. L. C.","last_name":"Miller"},{"full_name":"Conrady, D. G.","first_name":"D. G.","last_name":"Conrady"},{"first_name":"A. D.","last_name":"Barrow","full_name":"Barrow, A. D."},{"first_name":"D. Y.","last_name":"Chirgadze","full_name":"Chirgadze, D. Y."},{"first_name":"D.","last_name":"Bihan","full_name":"Bihan, D."},{"last_name":"Farndale","first_name":"R. W.","full_name":"Farndale, R. W."},{"full_name":"Herr, A. B.","first_name":"A. B.","last_name":"Herr"}],"publisher":"American Society of Hematology","intvolume":" 127","status":"public","title":"Structural basis for collagen recognition by the immune receptor OSCAR","publication_status":"published","pmid":1,"_id":"6507","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0006-4971","1528-0020"]},"day":"02","month":"11","language":[{"iso":"eng"}],"date_published":"2015-11-02T00:00:00Z","doi":"10.1182/blood-2015-08-667055","page":"529-537","quality_controlled":"1","external_id":{"pmid":["26552697"]},"citation":{"ieee":"L. Zhou et al., “Structural basis for collagen recognition by the immune receptor OSCAR,” Blood, vol. 127, no. 5. American Society of Hematology, pp. 529–537, 2015.","apa":"Zhou, L., Hinerman, J. M., Blaszczyk, M., Miller, J. L. C., Conrady, D. G., Barrow, A. D., … Herr, A. B. (2015). Structural basis for collagen recognition by the immune receptor OSCAR. Blood. American Society of Hematology. https://doi.org/10.1182/blood-2015-08-667055","ista":"Zhou L, Hinerman JM, Blaszczyk M, Miller JLC, Conrady DG, Barrow AD, Chirgadze DY, Bihan D, Farndale RW, Herr AB. 2015. Structural basis for collagen recognition by the immune receptor OSCAR. Blood. 127(5), 529–537.","ama":"Zhou L, Hinerman JM, Blaszczyk M, et al. Structural basis for collagen recognition by the immune receptor OSCAR. Blood. 2015;127(5):529-537. doi:10.1182/blood-2015-08-667055","chicago":"Zhou, Long, J. M. Hinerman, M. Blaszczyk, J. L. C. Miller, D. G. Conrady, A. D. Barrow, D. Y. Chirgadze, D. Bihan, R. W. Farndale, and A. B. Herr. “Structural Basis for Collagen Recognition by the Immune Receptor OSCAR.” Blood. American Society of Hematology, 2015. https://doi.org/10.1182/blood-2015-08-667055.","short":"L. Zhou, J.M. Hinerman, M. Blaszczyk, J.L.C. Miller, D.G. Conrady, A.D. Barrow, D.Y. Chirgadze, D. Bihan, R.W. Farndale, A.B. Herr, Blood 127 (2015) 529–537.","mla":"Zhou, Long, et al. “Structural Basis for Collagen Recognition by the Immune Receptor OSCAR.” Blood, vol. 127, no. 5, American Society of Hematology, 2015, pp. 529–37, doi:10.1182/blood-2015-08-667055."},"publication":"Blood"},{"_id":"6737","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","title":"Achieving Marton’s region for broadcast channels using polar codes","publication_status":"published","status":"public","publisher":"IEEE","intvolume":" 61","author":[{"first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"full_name":"Hassani, Hamed","first_name":"Hamed","last_name":"Hassani"},{"full_name":"Sason, Igal","last_name":"Sason","first_name":"Igal"},{"first_name":"Rudiger","last_name":"Urbanke","full_name":"Urbanke, Rudiger"}],"date_created":"2019-07-31T07:03:38Z","date_updated":"2021-01-12T08:08:46Z","oa_version":"Preprint","volume":61,"type":"journal_article","abstract":[{"lang":"eng","text":"This paper presents polar coding schemes for the two-user discrete memoryless broadcast channel (DM-BC) which achieve Marton's region with both common and private messages. This is the best achievable rate region known to date, and it is tight for all classes of two-user DM-BCs whose capacity regions are known. To accomplish this task, we first construct polar codes for both the superposition as well as binning strategy. By combining these two schemes, we obtain Marton's region with private messages only. Finally, we show how to handle the case of common information. The proposed coding schemes possess the usual advantages of polar codes, i.e., they have low encoding and decoding complexity and a superpolynomial decay rate of the error probability. We follow the lead of Goela, Abbe, and Gastpar, who recently introduced polar codes emulating the superposition and binning schemes. To align the polar indices, for both schemes, their solution involves some degradedness constraints that are assumed to hold between the auxiliary random variables and channel outputs. To remove these constraints, we consider the transmission of k blocks and employ a chaining construction that guarantees the proper alignment of the polarized indices. The techniques described in this paper are quite general, and they can be adopted to many other multiterminal scenarios whenever there polar indices need to be aligned."}],"issue":"2","extern":"1","publication":"IEEE Transactions on Information Theory","external_id":{"arxiv":["1401.6060"]},"main_file_link":[{"url":"https://arxiv.org/abs/1401.6060","open_access":"1"}],"oa":1,"citation":{"short":"M. Mondelli, H. Hassani, I. Sason, R. Urbanke, IEEE Transactions on Information Theory 61 (2015) 783–800.","mla":"Mondelli, Marco, et al. “Achieving Marton’s Region for Broadcast Channels Using Polar Codes.” IEEE Transactions on Information Theory, vol. 61, no. 2, IEEE, 2015, pp. 783–800, doi:10.1109/tit.2014.2368555.","chicago":"Mondelli, Marco, Hamed Hassani, Igal Sason, and Rudiger Urbanke. “Achieving Marton’s Region for Broadcast Channels Using Polar Codes.” IEEE Transactions on Information Theory. IEEE, 2015. https://doi.org/10.1109/tit.2014.2368555.","ama":"Mondelli M, Hassani H, Sason I, Urbanke R. Achieving Marton’s region for broadcast channels using polar codes. IEEE Transactions on Information Theory. 2015;61(2):783-800. doi:10.1109/tit.2014.2368555","ieee":"M. Mondelli, H. Hassani, I. Sason, and R. Urbanke, “Achieving Marton’s region for broadcast channels using polar codes,” IEEE Transactions on Information Theory, vol. 61, no. 2. IEEE, pp. 783–800, 2015.","apa":"Mondelli, M., Hassani, H., Sason, I., & Urbanke, R. (2015). Achieving Marton’s region for broadcast channels using polar codes. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/tit.2014.2368555","ista":"Mondelli M, Hassani H, Sason I, Urbanke R. 2015. Achieving Marton’s region for broadcast channels using polar codes. IEEE Transactions on Information Theory. 61(2), 783–800."},"quality_controlled":"1","page":"783-800","doi":"10.1109/tit.2014.2368555","date_published":"2015-02-01T00:00:00Z","language":[{"iso":"eng"}],"day":"01","month":"02"},{"day":"01","month":"09","page":"4838-4851","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1304.5220","open_access":"1"}],"oa":1,"citation":{"mla":"Mondelli, Marco, et al. “Scaling Exponent of List Decoders with Applications to Polar Codes.” IEEE Transactions on Information Theory, vol. 61, no. 9, IEEE, 2015, pp. 4838–51, doi:10.1109/tit.2015.2453315.","short":"M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory 61 (2015) 4838–4851.","chicago":"Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “Scaling Exponent of List Decoders with Applications to Polar Codes.” IEEE Transactions on Information Theory. IEEE, 2015. https://doi.org/10.1109/tit.2015.2453315.","ama":"Mondelli M, Hassani H, Urbanke R. Scaling exponent of list decoders with applications to polar codes. IEEE Transactions on Information Theory. 2015;61(9):4838-4851. doi:10.1109/tit.2015.2453315","ista":"Mondelli M, Hassani H, Urbanke R. 2015. Scaling exponent of list decoders with applications to polar codes. IEEE Transactions on Information Theory. 61(9), 4838–4851.","ieee":"M. Mondelli, H. Hassani, and R. Urbanke, “Scaling exponent of list decoders with applications to polar codes,” IEEE Transactions on Information Theory, vol. 61, no. 9. IEEE, pp. 4838–4851, 2015.","apa":"Mondelli, M., Hassani, H., & Urbanke, R. (2015). Scaling exponent of list decoders with applications to polar codes. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/tit.2015.2453315"},"external_id":{"arxiv":["1304.5220"]},"publication":"IEEE Transactions on Information Theory","language":[{"iso":"eng"}],"date_published":"2015-09-01T00:00:00Z","doi":"10.1109/tit.2015.2453315","type":"journal_article","extern":"1","issue":"9","abstract":[{"lang":"eng","text":"Motivated by the significant performance gains which polar codes experience under successive cancellation list decoding, their scaling exponent is studied as a function of the list size. In particular, the error probability is fixed, and the tradeoff between the block length and back-off from capacity is analyzed. A lower bound is provided on the error probability under MAP decoding with list size L for any binary-input memoryless output-symmetric channel and for any class of linear codes such that their minimum distance is unbounded as the block length grows large. Then, it is shown that under MAP decoding, although the introduction of a list can significantly improve the involved constants, the scaling exponent itself, i.e., the speed at which capacity is approached, stays unaffected for any finite list size. In particular, this result applies to polar codes, since their minimum distance tends to infinity as the block length increases. A similar result is proved for genie-aided successive cancellation decoding when transmission takes place over the binary erasure channel, namely, the scaling exponent remains constant for any fixed number of helps from the genie. Note that since genie-aided successive cancellation decoding might be strictly worse than successive cancellation list decoding, the problem of establishing the scaling exponent of the latter remains open."}],"publisher":"IEEE","intvolume":" 61","status":"public","title":"Scaling exponent of list decoders with applications to polar codes","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6736","year":"2015","volume":61,"oa_version":"Preprint","date_updated":"2021-01-12T08:08:45Z","date_created":"2019-07-31T06:50:34Z","author":[{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"},{"full_name":"Hassani, Hamed","first_name":"Hamed","last_name":"Hassani"},{"full_name":"Urbanke, Rudiger","first_name":"Rudiger","last_name":"Urbanke"}]},{"oa_version":"None","volume":92,"date_created":"2019-11-19T13:22:06Z","date_updated":"2021-01-12T08:11:42Z","author":[{"first_name":"Jing Fei","last_name":"Yu","full_name":"Yu, Jing Fei"},{"first_name":"B. J.","last_name":"Ramshaw","full_name":"Ramshaw, B. J."},{"last_name":"Kokanović","first_name":"I.","full_name":"Kokanović, I."},{"first_name":"Kimberly A","last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A"},{"full_name":"Harrison, N.","last_name":"Harrison","first_name":"N."},{"full_name":"Day, James","first_name":"James","last_name":"Day"},{"first_name":"Ruixing","last_name":"Liang","full_name":"Liang, Ruixing"},{"full_name":"Hardy, W. N.","last_name":"Hardy","first_name":"W. N."},{"first_name":"D. A.","last_name":"Bonn","full_name":"Bonn, D. A."},{"last_name":"McCollam","first_name":"A.","full_name":"McCollam, A."},{"full_name":"Julian, S. R.","last_name":"Julian","first_name":"S. R."},{"full_name":"Cooper, J. R.","first_name":"J. R.","last_name":"Cooper"}],"intvolume":" 92","publisher":"APS","publication_status":"published","title":"Magnetization of underdoped YBa2Cu3Oy above the irreversibility field","status":"public","year":"2015","_id":"7070","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","issue":"18","abstract":[{"lang":"eng","text":"Torque magnetization measurements on YBa2Cu3Oy (YBCO) at doping y=6.67 (p=0.12), in dc fields (B) up to 33 T and temperatures down to 4.5 K, show that weak diamagnetism persists above the extrapolated irreversibility field Hirr(T=0)≈24 T. The differential susceptibility dM/dB, however, is more rapidly suppressed for B≳16 T than expected from the properties of the low field superconducting state, and saturates at a low value for fields B≳24 T. In addition, torque measurements on a p=0.11 YBCO crystal in pulsed field up to 65 T and temperatures down to 8 K show similar behavior, with no additional features at higher fields. We offer two candidate scenarios to explain these observations: (a) superconductivity survives but is heavily suppressed at high field by competition with charge-density-wave (CDW) order; (b) static superconductivity disappears near 24 T and is followed by a region of fluctuating superconductivity, which causes dM/dB to saturate at high field. The diamagnetic signal observed above 50 T for the p=0.11 crystal at 40 K and below may be caused by changes in the normal state susceptibility rather than bulk or fluctuating superconductivity. There will be orbital (Landau) diamagnetism from electron pockets and possibly a reduction in spin susceptibility caused by the stronger three-dimensional ordered CDW."}],"type":"journal_article","article_number":"180509","language":[{"iso":"eng"}],"doi":"10.1103/physrevb.92.180509","date_published":"2015-11-23T00:00:00Z","quality_controlled":"1","article_type":"original","citation":{"mla":"Yu, Jing Fei, et al. “Magnetization of Underdoped YBa2Cu3Oy above the Irreversibility Field.” Physical Review B, vol. 92, no. 18, 180509, APS, 2015, doi:10.1103/physrevb.92.180509.","short":"J.F. Yu, B.J. Ramshaw, I. Kokanović, K.A. Modic, N. Harrison, J. Day, R. Liang, W.N. Hardy, D.A. Bonn, A. McCollam, S.R. Julian, J.R. Cooper, Physical Review B 92 (2015).","chicago":"Yu, Jing Fei, B. J. Ramshaw, I. Kokanović, Kimberly A Modic, N. Harrison, James Day, Ruixing Liang, et al. “Magnetization of Underdoped YBa2Cu3Oy above the Irreversibility Field.” Physical Review B. APS, 2015. https://doi.org/10.1103/physrevb.92.180509.","ama":"Yu JF, Ramshaw BJ, Kokanović I, et al. Magnetization of underdoped YBa2Cu3Oy above the irreversibility field. Physical Review B. 2015;92(18). doi:10.1103/physrevb.92.180509","ista":"Yu JF, Ramshaw BJ, Kokanović I, Modic KA, Harrison N, Day J, Liang R, Hardy WN, Bonn DA, McCollam A, Julian SR, Cooper JR. 2015. Magnetization of underdoped YBa2Cu3Oy above the irreversibility field. Physical Review B. 92(18), 180509.","apa":"Yu, J. F., Ramshaw, B. J., Kokanović, I., Modic, K. A., Harrison, N., Day, J., … Cooper, J. R. (2015). Magnetization of underdoped YBa2Cu3Oy above the irreversibility field. Physical Review B. APS. https://doi.org/10.1103/physrevb.92.180509","ieee":"J. F. Yu et al., “Magnetization of underdoped YBa2Cu3Oy above the irreversibility field,” Physical Review B, vol. 92, no. 18. APS, 2015."},"publication":"Physical Review B","publication_identifier":{"issn":["1098-0121","1550-235X"]},"article_processing_charge":"No","day":"23","month":"11"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7456","title":"Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals","status":"public","intvolume":" 7","oa_version":"None","type":"journal_article","abstract":[{"text":"The rational design of monodisperse ferroelectric nanocrystals with controlled size and shape and their organization into hierarchical structures has been a critical step for understanding the polar ordering in nanoscale ferroelectrics, as well as the design of nanocrystal-based functional materials which harness the properties of individual nanoparticles and the collective interactions between them. We report here on the synthesis and self-assembly of aggregate-free, single-crystalline titanium-based perovskite nanoparticles with controlled morphology and surface composition by using a simple, easily scalable and highly versatile colloidal route. Single-crystalline, non-aggregated BaTiO3 colloidal nanocrystals, used as a model system, have been prepared under solvothermal conditions at temperatures as low as 180 °C. The shape of the nanocrystals was tuned from spheroidal to cubic upon changing the polarity of the solvent, whereas their size was varied from 16 to 30 nm for spheres and 5 to 78 nm for cubes by changing the concentration of the precursors and the reaction time, respectively. The hydrophobic, oleic acid-passivated nanoparticles exhibit very good solubility in non-polar solvents and can be rendered dispersible in polar solvents by a simple process involving the oxidative cleavage of the double bond upon treating the nanopowders with the Lemieux–von Rudloff reagent. Lattice dynamic analysis indicated that regardless of their size, BaTiO3 nanocrystals present local disorder within the perovskite unit cell, associated with the existence of polar ordering. We also demonstrate for the first time that, in addition to being used for fabricating large area, crack-free, highly uniform films, BaTiO3 nanocubes can serve as building blocks for the design of 2D and 3D mesoscale structures, such as superlattices and superparticles. Interestingly, the type of superlattice structure (simple cubic or face centered cubic) appears to be determined by the type of solvent in which the nanocrystals were dispersed. This approach provides an excellent platform for the synthesis of other titanium-based perovskite colloidal nanocrystals with controlled chemical composition, surface structure and morphology and for their assembly into complex architectures, therefore opening the door for the design of novel mesoscale functional materials/nanocomposites with potential applications in energy conversion, data storage and the biomedical field.","lang":"eng"}],"issue":"30","publication":"Nanoscale","citation":{"chicago":"Caruntu, Daniela, Taha Rostamzadeh, Tommaso Costanzo, Saman Salemizadeh Parizi, and Gabriel Caruntu. “Solvothermal Synthesis and Controlled Self-Assembly of Monodisperse Titanium-Based Perovskite Colloidal Nanocrystals.” Nanoscale. RSC, 2015. https://doi.org/10.1039/c5nr00737b.","mla":"Caruntu, Daniela, et al. “Solvothermal Synthesis and Controlled Self-Assembly of Monodisperse Titanium-Based Perovskite Colloidal Nanocrystals.” Nanoscale, vol. 7, no. 30, RSC, 2015, pp. 12955–69, doi:10.1039/c5nr00737b.","short":"D. Caruntu, T. Rostamzadeh, T. Costanzo, S. Salemizadeh Parizi, G. Caruntu, Nanoscale 7 (2015) 12955–12969.","ista":"Caruntu D, Rostamzadeh T, Costanzo T, Salemizadeh Parizi S, Caruntu G. 2015. Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals. Nanoscale. 7(30), 12955–12969.","ieee":"D. Caruntu, T. Rostamzadeh, T. Costanzo, S. Salemizadeh Parizi, and G. Caruntu, “Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals,” Nanoscale, vol. 7, no. 30. RSC, pp. 12955–12969, 2015.","apa":"Caruntu, D., Rostamzadeh, T., Costanzo, T., Salemizadeh Parizi, S., & Caruntu, G. (2015). Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals. Nanoscale. RSC. https://doi.org/10.1039/c5nr00737b","ama":"Caruntu D, Rostamzadeh T, Costanzo T, Salemizadeh Parizi S, Caruntu G. Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based perovskite colloidal nanocrystals. Nanoscale. 2015;7(30):12955-12969. doi:10.1039/c5nr00737b"},"article_type":"original","page":"12955-12969","date_published":"2015-08-14T00:00:00Z","day":"14","article_processing_charge":"No","year":"2015","pmid":1,"publication_status":"published","publisher":"RSC","author":[{"first_name":"Daniela","last_name":"Caruntu","full_name":"Caruntu, Daniela"},{"full_name":"Rostamzadeh, Taha","first_name":"Taha","last_name":"Rostamzadeh"},{"last_name":"Costanzo","first_name":"Tommaso","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso"},{"first_name":"Saman","last_name":"Salemizadeh Parizi","full_name":"Salemizadeh Parizi, Saman"},{"first_name":"Gabriel","last_name":"Caruntu","full_name":"Caruntu, Gabriel"}],"date_updated":"2023-02-23T13:08:24Z","date_created":"2020-02-05T14:16:37Z","volume":7,"extern":"1","external_id":{"pmid":["26168304"]},"quality_controlled":"1","doi":"10.1039/c5nr00737b","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["2040-3364","2040-3372"]}},{"doi":"10.1039/c5ra11347d","date_published":"2015-09-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"RSC Advances","citation":{"ieee":"S. S. Parizi, G. Conley, T. Costanzo, B. Howell, A. Mellinger, and G. Caruntu, “Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors,” RSC Advances, vol. 5, no. 93. RSC, pp. 76356–76362, 2015.","apa":"Parizi, S. S., Conley, G., Costanzo, T., Howell, B., Mellinger, A., & Caruntu, G. (2015). Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors. RSC Advances. RSC. https://doi.org/10.1039/c5ra11347d","ista":"Parizi SS, Conley G, Costanzo T, Howell B, Mellinger A, Caruntu G. 2015. Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors. RSC Advances. 5(93), 76356–76362.","ama":"Parizi SS, Conley G, Costanzo T, Howell B, Mellinger A, Caruntu G. Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors. RSC Advances. 2015;5(93):76356-76362. doi:10.1039/c5ra11347d","chicago":"Parizi, Saman Salemizadeh, Gavin Conley, Tommaso Costanzo, Bob Howell, Axel Mellinger, and Gabriel Caruntu. “Fabrication of Barium Titanate/Acrylonitrile-Butadiene Styrene/Poly(Methyl Methacrylate) Nanocomposite Films for Hybrid Ferroelectric Capacitors.” RSC Advances. RSC, 2015. https://doi.org/10.1039/c5ra11347d.","short":"S.S. Parizi, G. Conley, T. Costanzo, B. Howell, A. Mellinger, G. Caruntu, RSC Advances 5 (2015) 76356–76362.","mla":"Parizi, Saman Salemizadeh, et al. “Fabrication of Barium Titanate/Acrylonitrile-Butadiene Styrene/Poly(Methyl Methacrylate) Nanocomposite Films for Hybrid Ferroelectric Capacitors.” RSC Advances, vol. 5, no. 93, RSC, 2015, pp. 76356–62, doi:10.1039/c5ra11347d."},"quality_controlled":"1","article_type":"original","page":"76356-76362","day":"01","month":"09","publication_identifier":{"issn":["2046-2069"]},"article_processing_charge":"No","author":[{"full_name":"Parizi, Saman Salemizadeh","last_name":"Parizi","first_name":"Saman Salemizadeh"},{"full_name":"Conley, Gavin","first_name":"Gavin","last_name":"Conley"},{"first_name":"Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso"},{"full_name":"Howell, Bob","first_name":"Bob","last_name":"Howell"},{"first_name":"Axel","last_name":"Mellinger","full_name":"Mellinger, Axel"},{"full_name":"Caruntu, Gabriel","first_name":"Gabriel","last_name":"Caruntu"}],"date_created":"2020-02-05T14:17:26Z","date_updated":"2023-02-23T13:08:26Z","volume":5,"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7457","year":"2015","title":"Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite films for hybrid ferroelectric capacitors","publication_status":"published","status":"public","publisher":"RSC","intvolume":" 5","abstract":[{"text":"A new organic–inorganic ferroelectric hybrid capacitor designed by uniformly incorporating surface modified monodisperse 15 nm ferroelectric BaTiO3 nanocubes into non-polar polymer blends of poly(methyl methacrylate) (PMMA) polymer and acrylonitrile-butadiene-styrene (ABS) terpolymer is described. The investigation of spatial distribution of nanofillers via a non-distractive thermal pulse method illustrates that the surface functionalization of nanocubes plays a key role in the uniform distribution of charge polarization within the polymer matrix. The discharged energy density of the nanocomposite with 30 vol% BaTiO3 nanocubes is ∼44 × 10−3 J cm−3, which is almost six times higher than that of the neat polymer. The facile processing, along with the superior mechanical and electrical properties of the BaTiO3/PMMA–ABS nanocomposites make them suitable for implementation into capacitive electrical energy storage devices.","lang":"eng"}],"issue":"93","extern":"1","type":"journal_article"},{"article_processing_charge":"No","publication_identifier":{"issn":["1061-4036","1546-1718"]},"day":"14","month":"09","citation":{"chicago":"Robinson, Matthew Richard, Gibran Hemani, Carolina Medina-Gomez, Massimo Mezzavilla, Tonu Esko, Konstantin Shakhbazov, Joseph E Powell, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” Nature Genetics. Springer Nature, 2015. https://doi.org/10.1038/ng.3401.","mla":"Robinson, Matthew Richard, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” Nature Genetics, vol. 47, no. 11, Springer Nature, 2015, pp. 1357–62, doi:10.1038/ng.3401.","short":"M.R. Robinson, G. Hemani, C. Medina-Gomez, M. Mezzavilla, T. Esko, K. Shakhbazov, J.E. Powell, A. Vinkhuyzen, S.I. Berndt, S. Gustafsson, A.E. Justice, B. Kahali, A.E. Locke, T.H. Pers, S. Vedantam, A.R. Wood, W. van Rheenen, O.A. Andreassen, P. Gasparini, A. Metspalu, L.H. van den Berg, J.H. Veldink, F. Rivadeneira, T.M. Werge, G.R. Abecasis, D.I. Boomsma, D.I. Chasman, E.J.C. de Geus, T.M. Frayling, J.N. Hirschhorn, J.J. Hottenga, E. Ingelsson, R.J.F. Loos, P.K.E. Magnusson, N.G. Martin, G.W. Montgomery, K.E. North, N.L. Pedersen, T.D. Spector, E.K. Speliotes, M.E. Goddard, J. Yang, P.M. Visscher, Nature Genetics 47 (2015) 1357–1362.","ista":"Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K, Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S, Justice AE, Kahali B, Locke AE, Pers TH, Vedantam S, Wood AR, van Rheenen W, Andreassen OA, Gasparini P, Metspalu A, Berg LH van den, Veldink JH, Rivadeneira F, Werge TM, Abecasis GR, Boomsma DI, Chasman DI, de Geus EJC, Frayling TM, Hirschhorn JN, Hottenga JJ, Ingelsson E, Loos RJF, Magnusson PKE, Martin NG, Montgomery GW, North KE, Pedersen NL, Spector TD, Speliotes EK, Goddard ME, Yang J, Visscher PM. 2015. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 47(11), 1357–1362.","ieee":"M. R. Robinson et al., “Population genetic differentiation of height and body mass index across Europe,” Nature Genetics, vol. 47, no. 11. Springer Nature, pp. 1357–1362, 2015.","apa":"Robinson, M. R., Hemani, G., Medina-Gomez, C., Mezzavilla, M., Esko, T., Shakhbazov, K., … Visscher, P. M. (2015). Population genetic differentiation of height and body mass index across Europe. Nature Genetics. Springer Nature. https://doi.org/10.1038/ng.3401","ama":"Robinson MR, Hemani G, Medina-Gomez C, et al. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 2015;47(11):1357-1362. doi:10.1038/ng.3401"},"publication":"Nature Genetics","page":"1357-1362","article_type":"original","quality_controlled":"1","doi":"10.1038/ng.3401","date_published":"2015-09-14T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","issue":"11","abstract":[{"text":"Across-nation differences in the mean values for complex traits are common1,2,3,4,5,6,7,8, but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95 × 10−4), and we find an among-population genetic correlation for tall and slender individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P < 0.001), but environmental differences across Europe masked genetic differentiation for BMI (P < 0.58).","lang":"eng"}],"extern":"1","year":"2015","_id":"7742","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","intvolume":" 47","publication_status":"published","status":"public","title":"Population genetic differentiation of height and body mass index across Europe","author":[{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"full_name":"Hemani, Gibran","first_name":"Gibran","last_name":"Hemani"},{"full_name":"Medina-Gomez, Carolina","first_name":"Carolina","last_name":"Medina-Gomez"},{"full_name":"Mezzavilla, Massimo","last_name":"Mezzavilla","first_name":"Massimo"},{"last_name":"Esko","first_name":"Tonu","full_name":"Esko, Tonu"},{"last_name":"Shakhbazov","first_name":"Konstantin","full_name":"Shakhbazov, Konstantin"},{"full_name":"Powell, Joseph E","last_name":"Powell","first_name":"Joseph E"},{"full_name":"Vinkhuyzen, Anna","first_name":"Anna","last_name":"Vinkhuyzen"},{"first_name":"Sonja I","last_name":"Berndt","full_name":"Berndt, Sonja I"},{"full_name":"Gustafsson, Stefan","last_name":"Gustafsson","first_name":"Stefan"},{"full_name":"Justice, Anne E","last_name":"Justice","first_name":"Anne E"},{"full_name":"Kahali, Bratati","first_name":"Bratati","last_name":"Kahali"},{"first_name":"Adam E","last_name":"Locke","full_name":"Locke, Adam E"},{"full_name":"Pers, Tune H","first_name":"Tune H","last_name":"Pers"},{"last_name":"Vedantam","first_name":"Sailaja","full_name":"Vedantam, Sailaja"},{"last_name":"Wood","first_name":"Andrew R","full_name":"Wood, Andrew R"},{"first_name":"Wouter","last_name":"van Rheenen","full_name":"van Rheenen, Wouter"},{"first_name":"Ole A","last_name":"Andreassen","full_name":"Andreassen, Ole A"},{"full_name":"Gasparini, Paolo","first_name":"Paolo","last_name":"Gasparini"},{"full_name":"Metspalu, Andres","last_name":"Metspalu","first_name":"Andres"},{"last_name":"Berg","first_name":"Leonard H van den","full_name":"Berg, Leonard H van den"},{"full_name":"Veldink, Jan H","first_name":"Jan H","last_name":"Veldink"},{"last_name":"Rivadeneira","first_name":"Fernando","full_name":"Rivadeneira, Fernando"},{"first_name":"Thomas M","last_name":"Werge","full_name":"Werge, Thomas M"},{"first_name":"Goncalo R","last_name":"Abecasis","full_name":"Abecasis, Goncalo R"},{"first_name":"Dorret I","last_name":"Boomsma","full_name":"Boomsma, Dorret I"},{"full_name":"Chasman, Daniel I","last_name":"Chasman","first_name":"Daniel I"},{"full_name":"de Geus, Eco J C","last_name":"de Geus","first_name":"Eco J C"},{"first_name":"Timothy M","last_name":"Frayling","full_name":"Frayling, Timothy M"},{"full_name":"Hirschhorn, Joel N","first_name":"Joel N","last_name":"Hirschhorn"},{"first_name":"Jouke Jan","last_name":"Hottenga","full_name":"Hottenga, Jouke Jan"},{"last_name":"Ingelsson","first_name":"Erik","full_name":"Ingelsson, Erik"},{"last_name":"Loos","first_name":"Ruth J F","full_name":"Loos, Ruth J F"},{"last_name":"Magnusson","first_name":"Patrik K E","full_name":"Magnusson, Patrik K E"},{"first_name":"Nicholas G","last_name":"Martin","full_name":"Martin, Nicholas G"},{"first_name":"Grant W","last_name":"Montgomery","full_name":"Montgomery, Grant W"},{"first_name":"Kari E","last_name":"North","full_name":"North, Kari E"},{"last_name":"Pedersen","first_name":"Nancy L","full_name":"Pedersen, Nancy L"},{"full_name":"Spector, Timothy D","last_name":"Spector","first_name":"Timothy D"},{"full_name":"Speliotes, Elizabeth K","first_name":"Elizabeth K","last_name":"Speliotes"},{"full_name":"Goddard, Michael E","last_name":"Goddard","first_name":"Michael E"},{"full_name":"Yang, Jian","last_name":"Yang","first_name":"Jian"},{"full_name":"Visscher, Peter M","last_name":"Visscher","first_name":"Peter M"}],"volume":47,"oa_version":"None","date_updated":"2021-01-12T08:15:13Z","date_created":"2020-04-30T10:58:23Z"},{"date_published":"2015-07-07T00:00:00Z","citation":{"ama":"Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 2015;282(1810). doi:10.1098/rspb.2015.0689","ista":"Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. 2015. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 282(1810), 20150689.","apa":"Adams, M. J., Robinson, M. R., Mannarelli, M.-E., & Hatchwell, B. J. (2015). Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2015.0689","ieee":"M. J. Adams, M. R. Robinson, M.-E. Mannarelli, and B. J. Hatchwell, “Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird,” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810. The Royal Society, 2015.","mla":"Adams, Mark James, et al. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810, 20150689, The Royal Society, 2015, doi:10.1098/rspb.2015.0689.","short":"M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings of the Royal Society B: Biological Sciences 282 (2015).","chicago":"Adams, Mark James, Matthew Richard Robinson, Maria-Elena Mannarelli, and Ben J. Hatchwell. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2015.0689."},"publication":"Proceedings of the Royal Society B: Biological Sciences","article_type":"original","article_processing_charge":"No","day":"07","oa_version":"Published Version","_id":"7741","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 282","status":"public","title":"Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird","issue":"1810","abstract":[{"lang":"eng","text":"Phenotypes expressed in a social context are not only a function of the individual, but can also be shaped by the phenotypes of social partners. These social effects may play a major role in the evolution of cooperative breeding if social partners differ in the quality of care they provide and if individual carers adjust their effort in relation to that of other carers. When applying social effects models to wild study systems, it is also important to explore sources of individual plasticity that could masquerade as social effects. We studied offspring provisioning rates of parents and helpers in a wild population of long-tailed tits Aegithalos caudatus using a quantitative genetic framework to identify these social effects and partition them into genetic, permanent environment and current environment components. Controlling for other effects, individuals were consistent in their provisioning effort at a given nest, but adjusted their effort based on who was in their social group, indicating the presence of social effects. However, these social effects differed between years and social contexts, indicating a current environment effect, rather than indicating a genetic or permanent environment effect. While this study reveals the importance of examining environmental and genetic sources of social effects, the framework we present is entirely general, enabling a greater understanding of potentially important social effects within any ecological population."}],"type":"journal_article","doi":"10.1098/rspb.2015.0689","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1098/rspb.2015.0689","open_access":"1"}],"external_id":{"pmid":["26063846"]},"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["0962-8452","1471-2954"]},"month":"07","author":[{"first_name":"Mark James","last_name":"Adams","full_name":"Adams, Mark James"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"first_name":"Maria-Elena","last_name":"Mannarelli","full_name":"Mannarelli, Maria-Elena"},{"full_name":"Hatchwell, Ben J.","first_name":"Ben J.","last_name":"Hatchwell"}],"volume":282,"date_created":"2020-04-30T10:58:07Z","date_updated":"2021-01-12T08:15:12Z","pmid":1,"year":"2015","publisher":"The Royal Society","publication_status":"published","extern":"1","article_number":"20150689"},{"_id":"7739","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","publisher":"Wiley","intvolume":" 24","status":"public","publication_status":"published","title":"Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations","author":[{"first_name":"Anna W.","last_name":"Santure","full_name":"Santure, Anna W."},{"full_name":"Poissant, Jocelyn","last_name":"Poissant","first_name":"Jocelyn"},{"last_name":"De Cauwer","first_name":"Isabelle","full_name":"De Cauwer, Isabelle"},{"last_name":"van Oers","first_name":"Kees","full_name":"van Oers, Kees"},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"},{"last_name":"Quinn","first_name":"John L.","full_name":"Quinn, John L."},{"first_name":"Martien A. M.","last_name":"Groenen","full_name":"Groenen, Martien A. M."},{"first_name":"Marcel E.","last_name":"Visser","full_name":"Visser, Marcel E."},{"full_name":"Sheldon, Ben C.","first_name":"Ben C.","last_name":"Sheldon"},{"full_name":"Slate, Jon","last_name":"Slate","first_name":"Jon"}],"volume":24,"oa_version":"Published Version","date_updated":"2021-01-12T08:15:12Z","date_created":"2020-04-30T10:51:01Z","type":"journal_article","abstract":[{"text":"Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long‐term studies across Europe and consequently are considered an ecological ‘model organism’. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long‐term study populations of great tits—one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population‐specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population‐specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free‐living populations.","lang":"eng"}],"extern":"1","citation":{"ama":"Santure AW, Poissant J, De Cauwer I, et al. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 2015;24:6148-6162. doi:10.1111/mec.13452","ista":"Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen MAM, Visser ME, Sheldon BC, Slate J. 2015. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 24, 6148–6162.","apa":"Santure, A. W., Poissant, J., De Cauwer, I., van Oers, K., Robinson, M. R., Quinn, J. L., … Slate, J. (2015). Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.13452","ieee":"A. W. Santure et al., “Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations,” Molecular Ecology, vol. 24. Wiley, pp. 6148–6162, 2015.","mla":"Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology, vol. 24, Wiley, 2015, pp. 6148–62, doi:10.1111/mec.13452.","short":"A.W. Santure, J. Poissant, I. De Cauwer, K. van Oers, M.R. Robinson, J.L. Quinn, M.A.M. Groenen, M.E. Visser, B.C. Sheldon, J. Slate, Molecular Ecology 24 (2015) 6148–6162.","chicago":"Santure, Anna W., Jocelyn Poissant, Isabelle De Cauwer, Kees van Oers, Matthew Richard Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser, Ben C. Sheldon, and Jon Slate. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology. Wiley, 2015. https://doi.org/10.1111/mec.13452."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.13452"}],"publication":"Molecular Ecology","page":"6148-6162","article_type":"original","quality_controlled":"1","doi":"10.1111/mec.13452","date_published":"2015-12-10T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["0962-1083"]},"month":"12","day":"10"},{"citation":{"ama":"Alistarh D-A, Kopinsky J, Li J, Shavit N. The SprayList: A scalable relaxed priority queue. In: Vol 2015-January. ACM; 2015:11-20. doi:10.1145/2688500.2688523","ista":"Alistarh D-A, Kopinsky J, Li J, Shavit N. 2015. The SprayList: A scalable relaxed priority queue. PPoPP: Principles and Practice of Parallel Pogramming vol. 2015–January, 11–20.","ieee":"D.-A. Alistarh, J. Kopinsky, J. Li, and N. Shavit, “The SprayList: A scalable relaxed priority queue,” presented at the PPoPP: Principles and Practice of Parallel Pogramming, 2015, vol. 2015–January, pp. 11–20.","apa":"Alistarh, D.-A., Kopinsky, J., Li, J., & Shavit, N. (2015). The SprayList: A scalable relaxed priority queue (Vol. 2015–January, pp. 11–20). Presented at the PPoPP: Principles and Practice of Parallel Pogramming, ACM. https://doi.org/10.1145/2688500.2688523","mla":"Alistarh, Dan-Adrian, et al. The SprayList: A Scalable Relaxed Priority Queue. Vol. 2015–January, ACM, 2015, pp. 11–20, doi:10.1145/2688500.2688523.","short":"D.-A. Alistarh, J. Kopinsky, J. Li, N. Shavit, in:, ACM, 2015, pp. 11–20.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Nir Shavit. “The SprayList: A Scalable Relaxed Priority Queue,” 2015–January:11–20. ACM, 2015. https://doi.org/10.1145/2688500.2688523."},"page":"11 - 20","conference":{"name":"PPoPP: Principles and Practice of Parallel Pogramming"},"date_published":"2015-01-24T00:00:00Z","doi":"10.1145/2688500.2688523","language":[{"iso":"eng"}],"month":"01","day":"24","article_processing_charge":"No","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle\r\nand Intel corporations.","_id":"776","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The SprayList: A scalable relaxed priority queue","status":"public","publication_status":"published","publisher":"ACM","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Kopinsky","first_name":"Justin","full_name":"Kopinsky, Justin"},{"full_name":"Li, Jerry","first_name":"Jerry","last_name":"Li"},{"first_name":"Nir","last_name":"Shavit","full_name":"Shavit, Nir"}],"date_created":"2018-12-11T11:48:26Z","date_updated":"2023-02-23T13:16:43Z","oa_version":"None","volume":"2015-January","type":"conference","abstract":[{"text":"High-performance concurrent priority queues are essential for applications such as task scheduling and discrete event simulation. Unfortunately, even the best performing implementations do not scale past a number of threads in the single digits. This is because of the sequential bottleneck in accessing the elements at the head of the queue in order to perform a DeleteMin operation. In this paper, we present the SprayList, a scalable priority queue with relaxed ordering semantics. Starting from a non-blocking SkipList, the main innovation behind our design is that the DeleteMin operations avoid a sequential bottleneck by "spraying" themselves onto the head of the SkipList list in a coordinated fashion. The spraying is implemented using a carefully designed random walk, so that DeleteMin returns an element among the first O(plog3p) in the list, with high probability, where p is the number of threads. We prove that the running time of a DeleteMin operation is O(log3p), with high probability, independent of the size of the list. Our experiments show that the relaxed semantics allow the data structure to scale for high thread counts, comparable to a classic unordered SkipList. Furthermore, we observe that, for reasonably parallel workloads, the scalability benefits of relaxation considerably outweigh the additional work due to out-of-order execution.","lang":"eng"}],"publist_id":"6878","extern":"1"},{"abstract":[{"lang":"eng","text":"We introduce a principle unique to disordered solids wherein the contribution of any bond to one global perturbation is uncorrelated with its contribution to another. Coupled with sufficient variability in the contributions of different bonds, this “independent bond-level response” paves the way for the design of real materials with unusual and exquisitely tuned properties. To illustrate this, we choose two global perturbations: compression and shear. By applying a bond removal procedure that is both simple and experimentally relevant to remove a very small fraction of bonds, we can drive disordered spring networks to both the incompressible and completely auxetic limits of mechanical behavior."}],"issue":"22","extern":"1","article_number":"225501","type":"journal_article","author":[{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"Liu","first_name":"Andrea J.","full_name":"Liu, Andrea J."},{"last_name":"Nagel","first_name":"Sidney R.","full_name":"Nagel, Sidney R."}],"date_updated":"2021-01-12T08:15:23Z","date_created":"2020-04-30T11:41:08Z","volume":114,"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7765","year":"2015","status":"public","title":"The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior","publication_status":"published","intvolume":" 114","publisher":"American Physical Society","day":"04","month":"06","article_processing_charge":"No","publication_identifier":{"issn":["0031-9007","1079-7114"]},"doi":"10.1103/physrevlett.114.225501","date_published":"2015-06-04T00:00:00Z","language":[{"iso":"eng"}],"publication":"Physical Review Letters","citation":{"mla":"Goodrich, Carl Peter, et al. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters, vol. 114, no. 22, 225501, American Physical Society, 2015, doi:10.1103/physrevlett.114.225501.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015).","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/physrevlett.114.225501.","ama":"Goodrich CP, Liu AJ, Nagel SR. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 2015;114(22). doi:10.1103/physrevlett.114.225501","ista":"Goodrich CP, Liu AJ, Nagel SR. 2015. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 114(22), 225501.","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior,” Physical Review Letters, vol. 114, no. 22. American Physical Society, 2015.","apa":"Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.114.225501"},"article_type":"original","quality_controlled":"1"},{"article_number":"032706","type":"journal_article","extern":"1","abstract":[{"text":"We present a model of soft active particles that leads to a rich array of collective behavior found also in dense biological swarms of bacteria and other unicellular organisms. Our model uses only local interactions, such as Vicsek-type nearest-neighbor alignment, short-range repulsion, and a local boundary term. Changing the relative strength of these interactions leads to migrating swarms, rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble motion, alternating between migration and either rotating or jammed states. Interestingly, although a migrating swarm moves slower than an individual particle, the diffusion constant can be up to three orders of magnitude larger, suggesting that collective motion can be highly advantageous, for example, when searching for food.","lang":"eng"}],"issue":"3","status":"public","title":"Collective dynamics of soft active particles","publication_status":"published","intvolume":" 91","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7767","year":"2015","date_updated":"2021-01-12T08:15:24Z","date_created":"2020-04-30T11:41:38Z","volume":91,"oa_version":"None","author":[{"full_name":"van Drongelen, Ruben","first_name":"Ruben","last_name":"van Drongelen"},{"last_name":"Pal","first_name":"Anshuman","full_name":"Pal, Anshuman"},{"last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter"},{"first_name":"Timon","last_name":"Idema","full_name":"Idema, Timon"}],"month":"03","day":"01","publication_identifier":{"issn":["1539-3755","1550-2376"]},"article_processing_charge":"No","article_type":"original","quality_controlled":"1","publication":"Physical Review E","citation":{"chicago":"Drongelen, Ruben van, Anshuman Pal, Carl Peter Goodrich, and Timon Idema. “Collective Dynamics of Soft Active Particles.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/physreve.91.032706.","short":"R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).","mla":"van Drongelen, Ruben, et al. “Collective Dynamics of Soft Active Particles.” Physical Review E, vol. 91, no. 3, 032706, American Physical Society, 2015, doi:10.1103/physreve.91.032706.","ieee":"R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema, “Collective dynamics of soft active particles,” Physical Review E, vol. 91, no. 3. American Physical Society, 2015.","apa":"van Drongelen, R., Pal, A., Goodrich, C. P., & Idema, T. (2015). Collective dynamics of soft active particles. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.91.032706","ista":"van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of soft active particles. Physical Review E. 91(3), 032706.","ama":"van Drongelen R, Pal A, Goodrich CP, Idema T. Collective dynamics of soft active particles. Physical Review E. 2015;91(3). doi:10.1103/physreve.91.032706"},"language":[{"iso":"eng"}],"date_published":"2015-03-01T00:00:00Z","doi":"10.1103/physreve.91.032706"},{"publication_identifier":{"issn":["1744-683X","1744-6848"]},"article_processing_charge":"No","month":"02","day":"15","page":"2745-2751","article_type":"original","quality_controlled":"1","citation":{"chicago":"Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4sm02905d.","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015) 2745–2751.","mla":"Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter, vol. 11, no. 14, Royal Society of Chemistry, 2015, pp. 2745–51, doi:10.1039/c4sm02905d.","apa":"Sussman, D. M., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). Disordered surface vibrations in jammed sphere packings. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c4sm02905d","ieee":"D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface vibrations in jammed sphere packings,” Soft Matter, vol. 11, no. 14. Royal Society of Chemistry, pp. 2745–2751, 2015.","ista":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations in jammed sphere packings. Soft Matter. 11(14), 2745–2751.","ama":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in jammed sphere packings. Soft Matter. 2015;11(14):2745-2751. doi:10.1039/c4sm02905d"},"publication":"Soft Matter","language":[{"iso":"eng"}],"date_published":"2015-02-15T00:00:00Z","doi":"10.1039/c4sm02905d","type":"journal_article","extern":"1","issue":"14","abstract":[{"lang":"eng","text":"We study the vibrational properties near a free surface of disordered spring networks derived from jammed sphere packings. In bulk systems, without surfaces, it is well understood that such systems have a plateau in the density of vibrational modes extending down to a frequency scale ω*. This frequency is controlled by ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres and twice the spatial dimension, d, of the system, which vanishes at the jamming transition. In the presence of a free surface we find that there is a density of disordered vibrational modes associated with the surface that extends far below ω*. The total number of these low-frequency surface modes is controlled by ΔZ, and the profile of their decay into the bulk has two characteristic length scales, which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached."}],"publisher":"Royal Society of Chemistry","intvolume":" 11","title":"Disordered surface vibrations in jammed sphere packings","publication_status":"published","status":"public","year":"2015","_id":"7766","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":11,"date_updated":"2021-01-12T08:15:23Z","date_created":"2020-04-30T11:41:23Z","author":[{"full_name":"Sussman, Daniel M.","last_name":"Sussman","first_name":"Daniel M."},{"first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"first_name":"Sidney R.","last_name":"Nagel","full_name":"Nagel, Sidney R."}]},{"month":"01","day":"01","article_processing_charge":"No","page":"1900 - 1908","main_file_link":[{"url":"http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning"}],"citation":{"apa":"Alistarh, D.-A., Iglesias, J., & Vojnović, M. (2015). Streaming min-max hypergraph partitioning (Vol. 2015–January, pp. 1900–1908). Presented at the NIPS: Neural Information Processing Systems, Neural Information Processing Systems.","ieee":"D.-A. Alistarh, J. Iglesias, and M. Vojnović, “Streaming min-max hypergraph partitioning,” presented at the NIPS: Neural Information Processing Systems, 2015, vol. 2015–January, pp. 1900–1908.","ista":"Alistarh D-A, Iglesias J, Vojnović M. 2015. Streaming min-max hypergraph partitioning. NIPS: Neural Information Processing Systems vol. 2015–January, 1900–1908.","ama":"Alistarh D-A, Iglesias J, Vojnović M. Streaming min-max hypergraph partitioning. In: Vol 2015-January. Neural Information Processing Systems; 2015:1900-1908.","chicago":"Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing Systems, 2015.","short":"D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing Systems, 2015, pp. 1900–1908.","mla":"Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning. Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08."},"language":[{"iso":"eng"}],"conference":{"name":"NIPS: Neural Information Processing Systems"},"date_published":"2015-01-01T00:00:00Z","type":"conference","extern":"1","abstract":[{"text":"In many applications, the data is of rich structure that can be represented by a hypergraph, where the data items are represented by vertices and the associations among items are represented by hyperedges. Equivalently, we are given an input bipartite graph with two types of vertices: items, and associations (which we refer to as topics). We consider the problem of partitioning the set of items into a given number of components such that the maximum number of topics covered by a component is minimized. This is a clustering problem with various applications, e.g. partitioning of a set of information objects such as documents, images, and videos, and load balancing in the context of modern computation platforms.Inthis paper, we focus on the streaming computation model for this problem, in which items arrive online one at a time and each item must be assigned irrevocably to a component at its arrival time. Motivated by scalability requirements, we focus on the class of streaming computation algorithms with memory limited to be at most linear in the number of components. We show that a greedy assignment strategy is able to recover a hidden co-clustering of items under a natural set of recovery conditions. We also report results of an extensive empirical evaluation, which demonstrate that this greedy strategy yields superior performance when compared with alternative approaches.","lang":"eng"}],"publist_id":"6879","title":"Streaming min-max hypergraph partitioning","status":"public","publication_status":"published","publisher":"Neural Information Processing Systems","_id":"777","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:48:27Z","date_updated":"2023-02-23T13:17:09Z","volume":"2015-January","oa_version":"None","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Iglesias, Jennifer","first_name":"Jennifer","last_name":"Iglesias"},{"last_name":"Vojnović","first_name":"Milan","full_name":"Vojnović, Milan"}]},{"abstract":[{"lang":"eng","text":"Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed to complement the fast, but best-effort nature of Hardware Transactional Memory (HTM) with a slow, reliable software backup. However, the costs of providing concurrency between hardware and software transactions in HyTM are still not well understood. In this paper, we propose a general model for HyTM implementations, which captures the ability of hardware transactions to buffer memory accesses. The model allows us to formally quantify and analyze the amount of overhead (instrumentation) caused by the potential presence of software transactions.We prove that (1) it is impossible to build a strictly serializable HyTM implementation that has both uninstrumented reads and writes, even for very weak progress guarantees, and (2) the instrumentation cost incurred by a hardware transaction in any progressive opaque HyTM is linear in the size of the transaction’s data set.We further describe two implementations which exhibit optimal instrumentation costs for two different progress conditions. In sum, this paper proposes the first formal HyTM model and captures for the first time the trade-off between the degree of hardware-software TM concurrency and the amount of instrumentation overhead."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","_id":"778","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Inherent limitations of hybrid transactional memory","status":"public","intvolume":" 9363","day":"01","article_processing_charge":"No","date_published":"2015-01-01T00:00:00Z","citation":{"mla":"Alistarh, Dan-Adrian, et al. Inherent Limitations of Hybrid Transactional Memory. Vol. 9363, Springer, 2015, pp. 185–99, doi:10.1007/978-3-662-48653-5_13.","short":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer, 2015, pp. 185–199.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Petr Kuznetsov, Srivatsan Ravi, and Nir Shavit. “Inherent Limitations of Hybrid Transactional Memory,” 9363:185–99. Springer, 2015. https://doi.org/10.1007/978-3-662-48653-5_13.","ama":"Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. Inherent limitations of hybrid transactional memory. In: Vol 9363. Springer; 2015:185-199. doi:10.1007/978-3-662-48653-5_13","ista":"Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. 2015. Inherent limitations of hybrid transactional memory. DISC: Distributed Computing, LNCS, vol. 9363, 185–199.","apa":"Alistarh, D.-A., Kopinsky, J., Kuznetsov, P., Ravi, S., & Shavit, N. (2015). Inherent limitations of hybrid transactional memory (Vol. 9363, pp. 185–199). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-662-48653-5_13","ieee":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, and N. Shavit, “Inherent limitations of hybrid transactional memory,” presented at the DISC: Distributed Computing, 2015, vol. 9363, pp. 185–199."},"page":"185 - 199","publist_id":"6880","extern":"1","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Kopinsky","first_name":"Justin","full_name":"Kopinsky, Justin"},{"full_name":"Kuznetsov, Petr","last_name":"Kuznetsov","first_name":"Petr"},{"first_name":"Srivatsan","last_name":"Ravi","full_name":"Ravi, Srivatsan"},{"first_name":"Nir","last_name":"Shavit","full_name":"Shavit, Nir"}],"date_updated":"2023-02-23T13:17:35Z","date_created":"2018-12-11T11:48:27Z","volume":9363,"year":"2015","acknowledgement":"P. Kuznetsov-The author is supported by the Agence Nationale de la Recherche, ANR-14-CE35-0010-01, project DISCMAT. N. Shavit-Support is gratfeully acknowledgedfrom the National Science Foundation under grants CCF-1217921, CCF-1201926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.","publication_status":"published","publisher":"Springer","month":"01","conference":{"name":"DISC: Distributed Computing"},"doi":"10.1007/978-3-662-48653-5_13","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1405.5689","open_access":"1"}],"external_id":{"arxiv":["1405.5689"]},"quality_controlled":"1"},{"oa_version":"Preprint","date_updated":"2021-01-12T08:15:28Z","date_created":"2020-04-30T12:16:18Z","author":[{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"}],"status":"public","title":"Unearthing the anticrystal: Criticality in the linear response of disordered solids","publication_status":"published","year":"2015","_id":"7779","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"text":"The fact that a disordered material is not constrained in its properties in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential for novel material design. However, unlike their crystalline\r\ncounterparts, disordered solids are not well understood. One of the primary\r\nobstacles is the lack of a theoretical framework for thinking about disorder\r\nand its relation to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition with diverging length scales and clean power-law\r\nsignatures. This critical point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the potential to provide the essential theoretical\r\nfoundation necessary for a unified understanding of the mechanics of disordered\r\nsolids. We begin by showing that jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact nonlinearities.\" We then investigate\r\nthe critical nature of the transition, focusing on diverging length scales and\r\nfinite-size effects. Next, we argue that jamming plays the same role for\r\ndisordered solids as the perfect crystal plays for crystalline solids. Not only\r\ncan it be considered an idealized starting point for understanding disordered\r\nmaterials, but it can even influence systems that have a relatively high amount\r\nof crystalline order. The behavior of solids can thus be thought of as existing\r\non a spectrum, with the perfect crystal and the jamming transition at opposing\r\nends. Finally, we introduce a new principle wherein the contribution of an\r\nindividual bond to one global property is independent of its contribution to\r\nanother. This principle allows the different global responses of a disordered\r\nsystem to be manipulated independently and provides a great deal of flexibility\r\nin designing materials with unique, textured and tunable properties.","lang":"eng"}],"type":"preprint","language":[{"iso":"eng"}],"date_published":"2015-10-29T00:00:00Z","page":"242","oa":1,"external_id":{"arxiv":["1510.08820"]},"main_file_link":[{"url":"https://arxiv.org/abs/1510.08820","open_access":"1"}],"citation":{"chicago":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.","mla":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.","short":"C.P. Goodrich, ArXiv:1510.08820 (2015).","ista":"Goodrich CP. 2015. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:1510.08820, .","apa":"Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:1510.08820.","ieee":"C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response of disordered solids,” arXiv:1510.08820. 2015.","ama":"Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:151008820. 2015."},"publication":"arXiv:1510.08820","article_processing_charge":"No","month":"10","day":"29"},{"author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Matveev, Alexander","last_name":"Matveev","first_name":"Alexander"},{"full_name":"Leiserson, William","last_name":"Leiserson","first_name":"William"},{"first_name":"Nir","last_name":"Shavit","full_name":"Shavit, Nir"}],"related_material":{"record":[{"id":"6001","status":"public","relation":"later_version"}]},"date_updated":"2023-02-23T12:35:42Z","date_created":"2018-12-11T11:48:27Z","oa_version":"None","volume":"2015-June","_id":"779","year":"2015","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle corporation. In particular, we would like to thank Dave Dice, Alex Kogan, and Mark Moir from the Oracle Scalable Synchronization Research Group for very useful feedback on earlier drafts of this paper.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"ThreadScan: Automatic and scalable memory reclamation","publisher":"ACM","abstract":[{"text":"The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU, are either prohibitively expensive or require significant programming expertise, to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated. In this paper, we take a new approach to concurrent memory reclamation: instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads. Initial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free.","lang":"eng"}],"publist_id":"6876","extern":"1","type":"conference","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"doi":"10.1145/2755573.2755600","date_published":"2015-06-13T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Alistarh D-A, Matveev A, Leiserson W, Shavit N. ThreadScan: Automatic and scalable memory reclamation. In: Vol 2015-June. ACM; 2015:123-132. doi:10.1145/2755573.2755600","ieee":"D.-A. Alistarh, A. Matveev, W. Leiserson, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, 2015, vol. 2015–June, pp. 123–132.","apa":"Alistarh, D.-A., Matveev, A., Leiserson, W., & Shavit, N. (2015). ThreadScan: Automatic and scalable memory reclamation (Vol. 2015–June, pp. 123–132). Presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. https://doi.org/10.1145/2755573.2755600","ista":"Alistarh D-A, Matveev A, Leiserson W, Shavit N. 2015. ThreadScan: Automatic and scalable memory reclamation. SPAA: Symposium on Parallelism in Algorithms and Architectures vol. 2015–June, 123–132.","short":"D.-A. Alistarh, A. Matveev, W. Leiserson, N. Shavit, in:, ACM, 2015, pp. 123–132.","mla":"Alistarh, Dan-Adrian, et al. ThreadScan: Automatic and Scalable Memory Reclamation. Vol. 2015–June, ACM, 2015, pp. 123–32, doi:10.1145/2755573.2755600.","chicago":"Alistarh, Dan-Adrian, Alexander Matveev, William Leiserson, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation,” 2015–June:123–32. ACM, 2015. https://doi.org/10.1145/2755573.2755600."},"page":"123 - 132","month":"06","day":"13","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-47666-6_38","date_published":"2015-01-01T00:00:00Z","conference":{"name":"ICALP: International Colloquium on Automota, Languages and Programming"},"page":"479 - 491","citation":{"ama":"Alistarh D-A, Gelashvili R. Polylogarithmic-time leader election in population protocols. In: Vol 9135. Springer; 2015:479-491. doi:10.1007/978-3-662-47666-6_38","apa":"Alistarh, D.-A., & Gelashvili, R. (2015). Polylogarithmic-time leader election in population protocols (Vol. 9135, pp. 479–491). Presented at the ICALP: International Colloquium on Automota, Languages and Programming, Springer. https://doi.org/10.1007/978-3-662-47666-6_38","ieee":"D.-A. Alistarh and R. Gelashvili, “Polylogarithmic-time leader election in population protocols,” presented at the ICALP: International Colloquium on Automota, Languages and Programming, 2015, vol. 9135, pp. 479–491.","ista":"Alistarh D-A, Gelashvili R. 2015. Polylogarithmic-time leader election in population protocols. ICALP: International Colloquium on Automota, Languages and Programming vol. 9135, 479–491.","short":"D.-A. Alistarh, R. Gelashvili, in:, Springer, 2015, pp. 479–491.","mla":"Alistarh, Dan-Adrian, and Rati Gelashvili. Polylogarithmic-Time Leader Election in Population Protocols. Vol. 9135, Springer, 2015, pp. 479–91, doi:10.1007/978-3-662-47666-6_38.","chicago":"Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader Election in Population Protocols,” 9135:479–91. Springer, 2015. https://doi.org/10.1007/978-3-662-47666-6_38."},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1502.05745","open_access":"1"}],"external_id":{"arxiv":["1502.05745"]},"day":"01","month":"01","volume":9135,"oa_version":"Preprint","date_updated":"2023-02-23T13:18:11Z","date_created":"2018-12-11T11:48:28Z","author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"}],"intvolume":" 9135","publisher":"Springer","title":"Polylogarithmic-time leader election in population protocols","publication_status":"published","status":"public","_id":"780","year":"2015","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.”","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","publist_id":"6877","abstract":[{"text":"Population protocols are networks of finite-state agents, interacting randomly, and updating their states using simple rules. Despite their extreme simplicity, these systems have been shown to cooperatively perform complex computational tasks, such as simulating register machines to compute standard arithmetic functions. The election of a unique leader agent is a key requirement in such computational constructions. Yet, the fastest currently known population protocol for electing a leader only has linear convergence time, and it has recently been shown that no population protocol using a constant number of states per node may overcome this linear bound. In this paper, we give the first population protocol for leader election with polylogarithmic convergence time, using polylogarithmic memory states per node. The protocol structure is quite simple: each node has an associated value, and is either a leader (still in contention) or a minion (following some leader). A leader keeps incrementing its value and “defeats” other leaders in one-to-one interactions, and will drop from contention and become a minion if it meets a leader with higher value. Importantly, a leader also drops out if it meets a minion with higher absolute value. While these rules are quite simple, the proof that this algorithm achieves polylogarithmic convergence time is non-trivial. In particular, the argument combines careful use of concentration inequalities with anti-concentration bounds, showing that the leaders’ values become spread apart as the execution progresses, which in turn implies that straggling leaders get quickly eliminated. We complement our analysis with empirical results, showing that our protocol converges extremely fast, even for large network sizes.","lang":"eng"}],"type":"conference"},{"language":[{"iso":"eng"}],"date_published":"2015-07-21T00:00:00Z","doi":"10.1145/2767386.2767429","conference":{"name":"PODC: Principles of Distributed Computing"},"page":"47 - 56","citation":{"ama":"Alistarh D-A, Gelashvili R, Vojnović M. Fast and exact majority in population protocols. In: Vol 2015-July. ACM; 2015:47-56. doi:10.1145/2767386.2767429","ista":"Alistarh D-A, Gelashvili R, Vojnović M. 2015. Fast and exact majority in population protocols. PODC: Principles of Distributed Computing vol. 2015–July, 47–56.","apa":"Alistarh, D.-A., Gelashvili, R., & Vojnović, M. (2015). Fast and exact majority in population protocols (Vol. 2015–July, pp. 47–56). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767429","ieee":"D.-A. Alistarh, R. Gelashvili, and M. Vojnović, “Fast and exact majority in population protocols,” presented at the PODC: Principles of Distributed Computing, 2015, vol. 2015–July, pp. 47–56.","mla":"Alistarh, Dan-Adrian, et al. Fast and Exact Majority in Population Protocols. Vol. 2015–July, ACM, 2015, pp. 47–56, doi:10.1145/2767386.2767429.","short":"D.-A. Alistarh, R. Gelashvili, M. Vojnović, in:, ACM, 2015, pp. 47–56.","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Milan Vojnović. “Fast and Exact Majority in Population Protocols,” 2015–July:47–56. ACM, 2015. https://doi.org/10.1145/2767386.2767429."},"article_processing_charge":"No","day":"21","month":"07","volume":"2015-July","oa_version":"None","date_created":"2018-12-11T11:48:28Z","date_updated":"2023-02-23T13:18:35Z","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"full_name":"Vojnović, Milan","last_name":"Vojnović","first_name":"Milan"}],"publisher":"ACM","title":"Fast and exact majority in population protocols","publication_status":"published","status":"public","_id":"781","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","publist_id":"6873","abstract":[{"text":"Population protocols, roughly defined as systems consisting of large numbers of simple identical agents, interacting at random and updating their state following simple rules, are an important research topic at the intersection of distributed computing and biology. One of the fundamental tasks that a population protocol may solve is majority: each node starts in one of two states; the goal is for all nodes to reach a correct consensus on which of the two states was initially the majority. Despite considerable research effort, known protocols for this problem are either exact but slow (taking linear parallel time to converge), or fast but approximate (with non-zero probability of error). In this paper, we show that this trade-off between preciasion and speed is not inherent. We present a new protocol called Average and Conquer (AVC) that solves majority ex-actly in expected parallel convergence time O(log n/(sε) + log n log s), where n is the number of nodes, εn is the initial node advantage of the majority state, and s = Ω(log n log log n) is the number of states the protocol employs. This shows that the majority problem can be solved exactly in time poly-logarithmic in n, provided that the memory per node is s = Ω(1/ε + lognlog1/ε). On the negative side, we establish a lower bound of Ω(1/ε) on the expected paraallel convergence time for the case of four memory states per node, and a lower bound of Ω(logn) parallel time for protocols using any number of memory states per node.per node, and a lower bound of (log n) parallel time for protocols using any number of memory states per node.","lang":"eng"}],"type":"conference"},{"conference":{"name":"PODC: Principles of Distributed Computing"},"date_published":"2015-07-21T00:00:00Z","doi":"10.1145/2767386.2767430","language":[{"iso":"eng"}],"citation":{"ama":"Alistarh D-A, Sauerwald T, Vojnović M. Lock-Free algorithms under stochastic schedulers. In: Vol 2015-July. ACM; 2015:251-260. doi:10.1145/2767386.2767430","ieee":"D.-A. Alistarh, T. Sauerwald, and M. Vojnović, “Lock-Free algorithms under stochastic schedulers,” presented at the PODC: Principles of Distributed Computing, 2015, vol. 2015–July, pp. 251–260.","apa":"Alistarh, D.-A., Sauerwald, T., & Vojnović, M. (2015). Lock-Free algorithms under stochastic schedulers (Vol. 2015–July, pp. 251–260). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767430","ista":"Alistarh D-A, Sauerwald T, Vojnović M. 2015. Lock-Free algorithms under stochastic schedulers. PODC: Principles of Distributed Computing vol. 2015–July, 251–260.","short":"D.-A. Alistarh, T. Sauerwald, M. Vojnović, in:, ACM, 2015, pp. 251–260.","mla":"Alistarh, Dan-Adrian, et al. Lock-Free Algorithms under Stochastic Schedulers. Vol. 2015–July, ACM, 2015, pp. 251–60, doi:10.1145/2767386.2767430.","chicago":"Alistarh, Dan-Adrian, Thomas Sauerwald, and Milan Vojnović. “Lock-Free Algorithms under Stochastic Schedulers,” 2015–July:251–60. ACM, 2015. https://doi.org/10.1145/2767386.2767430."},"page":"251 - 260","month":"07","day":"21","article_processing_charge":"No","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"last_name":"Sauerwald","first_name":"Thomas","full_name":"Sauerwald, Thomas"},{"full_name":"Vojnović, Milan","last_name":"Vojnović","first_name":"Milan"}],"date_updated":"2023-02-23T13:18:50Z","date_created":"2018-12-11T11:48:28Z","volume":"2015-July","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"782","year":"2015","status":"public","title":"Lock-Free algorithms under stochastic schedulers","publication_status":"published","publisher":"ACM","abstract":[{"text":"In this work, we consider the following random process, mo- Tivated by the analysis of lock-free concurrent algorithms under high memory contention. In each round, a new scheduling step is allocated to one of n threads, according to a distribution p = (p1; p2; : : : ; pn), where thread i is scheduled with probability pi. When some thread first reaches a set threshold of executed steps, it registers a win, completing its current operation, and resets its step count to 1. At the same time, threads whose step count was close to the threshold also get reset because of the win, but to 0 steps, being penalized for almost winning. We are interested in two questions: how often does some thread complete an operation (system latency), and how often does a specific thread complete an operation (individual latency)? We provide asymptotically tight bounds for the system and individual latency of this general concurrency pattern, for arbitrary scheduling distributions p. Surprisingly, a sim- ple characterization exists: in expectation, the system will complete a new operation every Θ(1/p 2) steps, while thread i will complete a new operation every Θ(1/2=p i ) steps. The proof is interesting in its own right, as it requires a careful analysis of how the higher norms of the vector p inuence the thread step counts and latencies in this random process. Our result offers a simple connection between the scheduling distribution and the average performance of concurrent algorithms, which has several applications.","lang":"eng"}],"publist_id":"6874","extern":"1","type":"conference"},{"citation":{"ama":"Alistarh D-A, Gelashvili R, Vladu A. How to elect a leader faster than a tournament. In: Vol 2015-July. ACM; 2015:365-374. doi:10.1145/2767386.2767420","ieee":"D.-A. Alistarh, R. Gelashvili, and A. Vladu, “How to elect a leader faster than a tournament,” presented at the PODC: Principles of Distributed Computing, 2015, vol. 2015–July, pp. 365–374.","apa":"Alistarh, D.-A., Gelashvili, R., & Vladu, A. (2015). How to elect a leader faster than a tournament (Vol. 2015–July, pp. 365–374). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767420","ista":"Alistarh D-A, Gelashvili R, Vladu A. 2015. How to elect a leader faster than a tournament. PODC: Principles of Distributed Computing vol. 2015–July, 365–374.","short":"D.-A. Alistarh, R. Gelashvili, A. Vladu, in:, ACM, 2015, pp. 365–374.","mla":"Alistarh, Dan-Adrian, et al. How to Elect a Leader Faster than a Tournament. Vol. 2015–July, ACM, 2015, pp. 365–74, doi:10.1145/2767386.2767420.","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Adrian Vladu. “How to Elect a Leader Faster than a Tournament,” 2015–July:365–74. ACM, 2015. https://doi.org/10.1145/2767386.2767420."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.1001"}],"oa":1,"page":"365 - 374","date_published":"2015-07-21T00:00:00Z","doi":"10.1145/2767386.2767420","conference":{"name":"PODC: Principles of Distributed Computing"},"language":[{"iso":"eng"}],"article_processing_charge":"No","month":"07","day":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"783","year":"2015","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926,\r\nand IIS-1447786, the Department of Energy under grant\r\nER26116/DE-SC0008923, and the Oracle and Intel corporations.\r\nThe authors would like to thank Prof. Nir Shavit for ad-\r\nvice and encouragement during this work, and the anonymous reviewers for their very useful suggestions.","publisher":"ACM","status":"public","title":"How to elect a leader faster than a tournament","publication_status":"published","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"},{"first_name":"Adrian","last_name":"Vladu","full_name":"Vladu, Adrian"}],"volume":"2015-July","oa_version":"None","date_created":"2018-12-11T11:48:28Z","date_updated":"2023-02-23T13:18:55Z","type":"conference","publist_id":"6875","abstract":[{"text":"The problem of electing a leader from among n contenders is one of the fundamental questions in distributed computing. In its simplest formulation, the task is as follows: given n processors, all participants must eventually return a win or lose indication, such that a single contender may win. Despite a considerable amount of work on leader election, the following question is still open: can we elect a leader in an asynchronous fault-prone system faster than just running a Θ(log n)-time tournament, against a strong adaptive adversary? In this paper, we answer this question in the affirmative, improving on a decades-old upper bound. We introduce two new algorithmic ideas to reduce the time complexity of electing a leader to O(log∗ n), using O(n2) point-to-point messages. A non-trivial application of our algorithm is a new upper bound for the tight renaming problem, assigning n items to the n participants in expected O(log2 n) time and O(n2) messages. We complement our results with lower bound of Ω(n2) messages for solving these two problems, closing the question of their message complexity.","lang":"eng"}],"extern":"1"},{"type":"conference","extern":"1","abstract":[{"text":"We demonstrate an optical switch design that can scale up to a thousand ports with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our design uses a broadcast and select architecture, based on a passive star coupler and fast tunable transceivers. In addition we employ time division multiplexing to achieve very low switching latency. Our demo shows the feasibility of the switch data plane using a small testbed, comprising two transmitters and a receiver, connected through a star coupler.","lang":"eng"}],"publist_id":"6872","status":"public","title":"A high-radix, low-latency optical switch for data centers","publication_status":"published","publisher":"ACM","_id":"784","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","date_created":"2018-12-11T11:48:29Z","date_updated":"2023-02-23T13:18:57Z","oa_version":"None","author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Ballani, Hitesh","last_name":"Ballani","first_name":"Hitesh"},{"first_name":"Paolo","last_name":"Costa","full_name":"Costa, Paolo"},{"full_name":"Funnell, Adam","last_name":"Funnell","first_name":"Adam"},{"full_name":"Benjamin, Joshua","first_name":"Joshua","last_name":"Benjamin"},{"full_name":"Watts, Philip","first_name":"Philip","last_name":"Watts"},{"first_name":"Benn","last_name":"Thomsen","full_name":"Thomsen, Benn"}],"month":"01","day":"01","publication_identifier":{"isbn":["978-1-4503-3542-3"]},"quality_controlled":"1","page":"367 - 368","citation":{"ieee":"D.-A. Alistarh et al., “A high-radix, low-latency optical switch for data centers,” presented at the SIGCOMM: Special Interest Group on Data Communication, London, United Kindgdom, 2015, pp. 367–368.","apa":"Alistarh, D.-A., Ballani, H., Costa, P., Funnell, A., Benjamin, J., Watts, P., & Thomsen, B. (2015). A high-radix, low-latency optical switch for data centers (pp. 367–368). Presented at the SIGCOMM: Special Interest Group on Data Communication, London, United Kindgdom: ACM. https://doi.org/10.1145/2785956.2790035","ista":"Alistarh D-A, Ballani H, Costa P, Funnell A, Benjamin J, Watts P, Thomsen B. 2015. A high-radix, low-latency optical switch for data centers. SIGCOMM: Special Interest Group on Data Communication, 367–368.","ama":"Alistarh D-A, Ballani H, Costa P, et al. A high-radix, low-latency optical switch for data centers. In: ACM; 2015:367-368. doi:10.1145/2785956.2790035","chicago":"Alistarh, Dan-Adrian, Hitesh Ballani, Paolo Costa, Adam Funnell, Joshua Benjamin, Philip Watts, and Benn Thomsen. “A High-Radix, Low-Latency Optical Switch for Data Centers,” 367–68. ACM, 2015. https://doi.org/10.1145/2785956.2790035.","short":"D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts, B. Thomsen, in:, ACM, 2015, pp. 367–368.","mla":"Alistarh, Dan-Adrian, et al. A High-Radix, Low-Latency Optical Switch for Data Centers. ACM, 2015, pp. 367–68, doi:10.1145/2785956.2790035."},"language":[{"iso":"eng"}],"conference":{"name":"SIGCOMM: Special Interest Group on Data Communication","start_date":"2015-08-17","location":"London, United Kindgdom","end_date":"2015-08-21"},"doi":"10.1145/2785956.2790035","date_published":"2015-01-01T00:00:00Z"},{"scopus_import":1,"month":"12","day":"01","page":"1423 - 1430","quality_controlled":"1","external_id":{"pmid":["26306635"]},"citation":{"ama":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 2015;25(12):1423-1430. doi:10.1093/glycob/cwv059","apa":"Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., & Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. Oxford University Press. https://doi.org/10.1093/glycob/cwv059","ieee":"J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier, “Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” Glycobiology, vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.","ista":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 25(12), 1423–1430.","short":"J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier, Glycobiology 25 (2015) 1423–1430.","mla":"Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” Glycobiology, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30, doi:10.1093/glycob/cwv059.","chicago":"Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” Glycobiology. Oxford University Press, 2015. https://doi.org/10.1093/glycob/cwv059."},"publication":"Glycobiology","language":[{"iso":"eng"}],"doi":"10.1093/glycob/cwv059","date_published":"2015-12-01T00:00:00Z","type":"journal_article","publist_id":"6851","issue":"12","abstract":[{"text":"Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.","lang":"eng"}],"department":[{"_id":"CaHe"}],"publisher":"Oxford University Press","intvolume":" 25","publication_status":"published","status":"public","title":"Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"802","year":"2015","volume":25,"oa_version":"None","date_updated":"2021-01-12T08:16:33Z","date_created":"2018-12-11T11:48:35Z","author":[{"last_name":"Engel","first_name":"Jakob","full_name":"Engel, Jakob"},{"full_name":"Schmalhorst, Philipp S","first_name":"Philipp S","last_name":"Schmalhorst","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5795-0133"},{"first_name":"Anke","last_name":"Kruger","full_name":"Kruger, Anke"},{"first_name":"Christina","last_name":"Muller","full_name":"Muller, Christina"},{"full_name":"Buettner, Falk","last_name":"Buettner","first_name":"Falk"},{"full_name":"Routier, Françoise","last_name":"Routier","first_name":"Françoise"}]},{"month":"09","day":"22","publication":"Journal of Virology","citation":{"mla":"Schur, Florian KM, et al. “The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.” Journal of Virology, vol. 89, no. 20, ASM, 2015, pp. 10294–302, doi:10.1128/JVI.01502-15.","short":"F.K. Schur, R. Dick, W. Hagen, V. Vogt, J. Briggs, Journal of Virology 89 (2015) 10294–10302.","chicago":"Schur, Florian KM, Robert Dick, Wim Hagen, Volker Vogt, and John Briggs. “The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.” Journal of Virology. ASM, 2015. https://doi.org/10.1128/JVI.01502-15.","ama":"Schur FK, Dick R, Hagen W, Vogt V, Briggs J. The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. 2015;89(20):10294-10302. doi:10.1128/JVI.01502-15","ista":"Schur FK, Dick R, Hagen W, Vogt V, Briggs J. 2015. The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. 89(20), 10294–10302.","apa":"Schur, F. K., Dick, R., Hagen, W., Vogt, V., & Briggs, J. (2015). The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. ASM. https://doi.org/10.1128/JVI.01502-15","ieee":"F. K. Schur, R. Dick, W. Hagen, V. Vogt, and J. Briggs, “The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly,” Journal of Virology, vol. 89, no. 20. ASM, pp. 10294–10302, 2015."},"external_id":{"pmid":["26223638"]},"quality_controlled":"1","page":"10294 - 10302","doi":"10.1128/JVI.01502-15","date_published":"2015-09-22T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"The polyprotein Gag is the primary structural component of retroviruses. Gag consists of independently folded domains connected by flexible linkers. Interactions between the conserved capsid (CA) domains of Gag mediate formation of hexameric protein lattices that drive assembly of immature virus particles. Proteolytic cleavage of Gag by the viral protease (PR) is required for maturation of retroviruses from an immature form into an infectious form. Within the assembled Gag lattices of HIV-1 and Mason- Pfizer monkey virus (M-PMV), the C-terminal domain of CA adopts similar quaternary arrangements, while the N-terminal domain of CA is packed in very different manners. Here, we have used cryo-electron tomography and subtomogram averaging to study in vitro-assembled, immature virus-like Rous sarcoma virus (RSV) Gag particles and have determined the structure of CA and the surrounding regions to a resolution of ~8 Å. We found that the C-terminal domain of RSV CA is arranged similarly to HIV-1 and M-PMV, whereas the N-terminal domain of CA adopts a novel arrangement in which the upstream p10 domain folds back into the CA lattice. In this position the cleavage site between CA and p10 appears to be inaccessible to PR. Below CA, an extended density is consistent with the presence of a six-helix bundle formed by the spacer-peptide region. We have also assessed the affect of lattice assembly on proteolytic processing by exogenous PR. The cleavage between p10 and CA is indeed inhibited in the assembled lattice, a finding consistent with structural regulation of proteolytic maturation.\r\n","lang":"eng"}],"publist_id":"6837","issue":"20","extern":"1","_id":"815","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","pmid":1,"publication_status":"published","status":"public","title":"The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly","publisher":"ASM","intvolume":" 89","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian","last_name":"Schur","full_name":"Schur, Florian"},{"last_name":"Dick","first_name":"Robert","full_name":"Dick, Robert"},{"first_name":"Wim","last_name":"Hagen","full_name":"Hagen, Wim"},{"first_name":"Volker","last_name":"Vogt","full_name":"Vogt, Volker"},{"last_name":"Briggs","first_name":"John","full_name":"Briggs, John"}],"date_created":"2018-12-11T11:48:39Z","date_updated":"2021-01-12T08:17:09Z","oa_version":"None","volume":89},{"citation":{"short":"F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs, Nature 517 (2015) 505–508.","mla":"Schur, Florian KM, et al. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” Nature, vol. 517, no. 7535, Nature Publishing Group, 2015, pp. 505–08, doi:10.1038/nature13838.","chicago":"Schur, Florian KM, Wim Hagen, Michaela Rumlová, Tomáš Ruml, B Müller, Hans Kraüsslich, and John Briggs. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature13838.","ama":"Schur FK, Hagen W, Rumlová M, et al. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. 2015;517(7535):505-508. doi:10.1038/nature13838","apa":"Schur, F. K., Hagen, W., Rumlová, M., Ruml, T., Müller, B., Kraüsslich, H., & Briggs, J. (2015). Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13838","ieee":"F. K. Schur et al., “Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution,” Nature, vol. 517, no. 7535. Nature Publishing Group, pp. 505–508, 2015.","ista":"Schur FK, Hagen W, Rumlová M, Ruml T, Müller B, Kraüsslich H, Briggs J. 2015. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. 517(7535), 505–508."},"publication":"Nature","page":"505 - 508","quality_controlled":0,"date_published":"2015-01-22T00:00:00Z","doi":"10.1038/nature13838","month":"01","day":"22","year":"2015","_id":"814","acknowledgement":"This study was supported by Deutsche Forschungsgemeinschaft grants BR 3635/2-1 to J.A.G.B., KR 906/7-1 to H.-G.K. and by Grant Agency of the Czech Republic 14-15326S to M.R. The Briggs laboratory acknowledges financial support from the European Molecular Biology Laboratory and from the Chica und Heinz Schaller Stiftung. We thank B. Glass, M. Anders and S. Mattei for preparation of samples, and R. Hadravova, K. H. Bui, F. Thommen, M. Schorb, S. Dodonova, S. Glatt, P. Ulbrich and T. Bharat for technical support and/or discussion. This study was technically supported by the European Molecular Biology Laboratory IT services unit.","intvolume":" 517","publisher":"Nature Publishing Group","publication_status":"published","title":"Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution","status":"public","author":[{"full_name":"Florian Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian"},{"full_name":"Hagen, Wim J","first_name":"Wim","last_name":"Hagen"},{"full_name":"Rumlová, Michaela","last_name":"Rumlová","first_name":"Michaela"},{"full_name":"Ruml, Tomáš","last_name":"Ruml","first_name":"Tomáš"},{"last_name":"Müller","first_name":"B","full_name":"Müller B"},{"full_name":"Kraüsslich, Hans Georg","first_name":"Hans","last_name":"Kraüsslich"},{"full_name":"Briggs, John A","first_name":"John","last_name":"Briggs"}],"volume":517,"date_updated":"2021-01-12T08:17:08Z","date_created":"2018-12-11T11:48:39Z","type":"journal_article","issue":"7535","publist_id":"6836","abstract":[{"lang":"eng","text":"Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the infected cell, inducing budding and release of an immature particle. Second, Gag is cleaved by the viral protease, leading to internal rearrangement of the virus into the mature, infectious form. Immature and mature HIV-1 particles are heterogeneous in size and morphology, preventing high-resolution analysis of their protein arrangement in situ by conventional structural biology methods. Here we apply cryo-electron tomography and sub-tomogram averaging methods to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices. The resulting model reveals tertiary and quaternary structural interactions that mediate HIV-1 assembly. Strikingly, these interactions differ from those predicted by the current model based on in vitro-assembled arrays of Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference, we solve the structure of the capsid lattice within intact immature Mason-Pfizer monkey virus particles. Comparison with the immature HIV-1 structure reveals that retroviral capsid proteins, while having conserved tertiary structures, adopt different quaternary arrangements during virus assembly. The approach demonstrated here should be applicable to determine structures of other proteins at subnanometre resolution within heterogeneous environments."}],"extern":1},{"date_published":"2015-02-01T00:00:00Z","doi":"10.1016/j.jaci.2014.12.1263","language":[{"iso":"eng"}],"publication":"Journal of Allergy and Clinical Immunology","citation":{"mla":"Einhorn, Lukas, et al. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” Journal of Allergy and Clinical Immunology, vol. 135, no. 2, AB101, Elsevier, 2015, doi:10.1016/j.jaci.2014.12.1263.","short":"L. Einhorn, J. Singer, M. Muhr, A. Schoos, K. Oida, J. Singer, L. Panakova, K. Manzano-Szalai, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 135 (2015).","chicago":"Einhorn, Lukas, Judit Singer, Martina Muhr, Alexandra Schoos, Kumiko Oida, Josef Singer, Lucia Panakova, Krisztina Manzano-Szalai, and Erika Jensen-Jarolim. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” Journal of Allergy and Clinical Immunology. Elsevier, 2015. https://doi.org/10.1016/j.jaci.2014.12.1263.","ama":"Einhorn L, Singer J, Muhr M, et al. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. 2015;135(2). doi:10.1016/j.jaci.2014.12.1263","ista":"Einhorn L, Singer J, Muhr M, Schoos A, Oida K, Singer J, Panakova L, Manzano-Szalai K, Jensen-Jarolim E. 2015. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. 135(2), AB101.","apa":"Einhorn, L., Singer, J., Muhr, M., Schoos, A., Oida, K., Singer, J., … Jensen-Jarolim, E. (2015). Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. Elsevier. https://doi.org/10.1016/j.jaci.2014.12.1263","ieee":"L. Einhorn et al., “Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients,” Journal of Allergy and Clinical Immunology, vol. 135, no. 2. Elsevier, 2015."},"article_type":"original","quality_controlled":"1","month":"02","day":"01","publication_identifier":{"issn":["0091-6749"]},"article_processing_charge":"No","author":[{"full_name":"Einhorn, Lukas","first_name":"Lukas","last_name":"Einhorn"},{"orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas","first_name":"Judit","full_name":"Fazekas, Judit"},{"full_name":"Muhr, Martina","first_name":"Martina","last_name":"Muhr"},{"full_name":"Schoos, Alexandra","last_name":"Schoos","first_name":"Alexandra"},{"full_name":"Oida, Kumiko","last_name":"Oida","first_name":"Kumiko"},{"first_name":"Josef","last_name":"Singer","full_name":"Singer, Josef"},{"first_name":"Lucia","last_name":"Panakova","full_name":"Panakova, Lucia"},{"full_name":"Manzano-Szalai, Krisztina","last_name":"Manzano-Szalai","first_name":"Krisztina"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"}],"date_updated":"2021-01-12T08:17:42Z","date_created":"2020-08-10T11:54:09Z","volume":135,"oa_version":"None","year":"2015","_id":"8242","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients","intvolume":" 135","publisher":"Elsevier","issue":"2","extern":"1","article_number":"AB101","type":"journal_article"},{"date_created":"2018-12-11T11:48:44Z","date_updated":"2021-01-12T08:18:07Z","volume":5,"author":[{"full_name":"Peter Marhavy","last_name":"Marhavy","first_name":"Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Eva Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"publication_status":"published","title":"Real time analysis of lateral root organogenesis in arabidopsis","status":"public","intvolume":" 5","publisher":"Bio-protocol LLC","acknowledgement":"European Research Council with a Starting Independent Research grant: ERC-2007-Stg-207362-HCPO, Czech Science Foundation: GA13-39982S\nWe thank Matyas Fendrych for critical reading and comments. The protocol was developed based on previously published work of De Rybel et al. (2010) and Laskowski et al. (2008). ","_id":"832","year":"2015","extern":1,"abstract":[{"lang":"eng","text":"Plants maintain capacity to form new organs such as leaves, flowers, lateral shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs) originate from a few pericycle cells that acquire attributes of founder cells (FCs), undergo series of anticlinal divisions, and give rise to a few short initial cells. After initiation, coordinated cell division and differentiation occur, giving rise to lateral root primordia (LRP). Primordia continue to grow, emerge through the cortex and epidermal layers of the primary root, and finally a new apical meristem is established taking over the responsibility for growth of mature lateral roots [for detailed description of the individual stages of lateral root organogenesis see Malamy and Benfey (1997)]. To examine this highly dynamic developmental process and to investigate a role of various hormonal, genetic and environmental factors in the regulation of lateral root organogenesis, the real time imaging based analyses represent extremely powerful tools (Laskowski et al., 2008; De Smet et al., 2012; Marhavy et al., 2013 and 2014). Herein, we describe a protocol for real time lateral root primordia (LRP) analysis, which enables the monitoring of an onset of the specific gene expression and subcellular protein localization during primordia organogenesis, as well as the evaluation of the impact of genetic and environmental perturbations on LRP organogenesis."}],"issue":"8","publist_id":"6816","type":"journal_article","doi":"10.21769/BioProtoc.1446","date_published":"2015-04-20T00:00:00Z","quality_controlled":0,"publication":"Bio-protocol","citation":{"short":"P. Marhavý, E. Benková, Bio-Protocol 5 (2015).","mla":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” Bio-Protocol, vol. 5, no. 8, Bio-protocol LLC, 2015, doi:10.21769/BioProtoc.1446.","chicago":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” Bio-Protocol. Bio-protocol LLC, 2015. https://doi.org/10.21769/BioProtoc.1446.","ama":"Marhavý P, Benková E. Real time analysis of lateral root organogenesis in arabidopsis. Bio-protocol. 2015;5(8). doi:10.21769/BioProtoc.1446","ieee":"P. Marhavý and E. Benková, “Real time analysis of lateral root organogenesis in arabidopsis,” Bio-protocol, vol. 5, no. 8. Bio-protocol LLC, 2015.","apa":"Marhavý, P., & Benková, E. (2015). Real time analysis of lateral root organogenesis in arabidopsis. Bio-Protocol. Bio-protocol LLC. https://doi.org/10.21769/BioProtoc.1446","ista":"Marhavý P, Benková E. 2015. Real time analysis of lateral root organogenesis in arabidopsis. Bio-protocol. 5(8)."},"day":"20","month":"04"},{"extern":"1","abstract":[{"lang":"eng","text":"The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments."}],"type":"journal_article","article_number":"8361","oa_version":"Published Version","volume":6,"date_updated":"2021-01-12T08:19:24Z","date_created":"2020-09-18T10:07:36Z","author":[{"full_name":"Ma, Peixiang","first_name":"Peixiang","last_name":"Ma"},{"full_name":"Xue, Yi","last_name":"Xue","first_name":"Yi"},{"last_name":"Coquelle","first_name":"Nicolas","full_name":"Coquelle, Nicolas"},{"full_name":"Haller, Jens D.","first_name":"Jens D.","last_name":"Haller"},{"last_name":"Yuwen","first_name":"Tairan","full_name":"Yuwen, Tairan"},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"last_name":"Mikhailovskii","first_name":"Oleg","full_name":"Mikhailovskii, Oleg"},{"full_name":"Willbold, Dieter","first_name":"Dieter","last_name":"Willbold"},{"first_name":"Jacques-Philippe","last_name":"Colletier","full_name":"Colletier, Jacques-Philippe"},{"last_name":"Skrynnikov","first_name":"Nikolai R.","full_name":"Skrynnikov, Nikolai R."},{"full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"intvolume":" 6","publisher":"Springer Nature","status":"public","title":"Observing the overall rocking motion of a protein in a crystal","publication_status":"published","year":"2015","_id":"8456","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"No","month":"10","day":"05","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"language":[{"iso":"eng"}],"date_published":"2015-10-05T00:00:00Z","doi":"10.1038/ncomms9361","article_type":"original","quality_controlled":"1","citation":{"short":"P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii, D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 6 (2015).","mla":"Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015, doi:10.1038/ncomms9361.","chicago":"Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361.","ama":"Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361","ieee":"P. Ma et al., “Observing the overall rocking motion of a protein in a crystal,” Nature Communications, vol. 6. Springer Nature, 2015.","apa":"Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda, P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms9361","ista":"Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 6, 8361."},"publication":"Nature Communications"},{"language":[{"iso":"eng"}],"date_published":"2015-09-10T00:00:00Z","doi":"10.1002/9780470034590.emrstm1418","article_type":"original","quality_controlled":"1","page":"699-708","publication":"eMagRes","citation":{"mla":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes, vol. 4, no. 3, Wiley, 2015, pp. 699–708, doi:10.1002/9780470034590.emrstm1418.","short":"P. Ma, P. Schanda, EMagRes 4 (2015) 699–708.","chicago":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes. Wiley, 2015. https://doi.org/10.1002/9780470034590.emrstm1418.","ama":"Ma P, Schanda P. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 2015;4(3):699-708. doi:10.1002/9780470034590.emrstm1418","ista":"Ma P, Schanda P. 2015. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 4(3), 699–708.","apa":"Ma, P., & Schanda, P. (2015). Conformational exchange processes in biological systems: Detection by solid-state NMR. EMagRes. Wiley. https://doi.org/10.1002/9780470034590.emrstm1418","ieee":"P. Ma and P. Schanda, “Conformational exchange processes in biological systems: Detection by solid-state NMR,” eMagRes, vol. 4, no. 3. Wiley, pp. 699–708, 2015."},"day":"10","month":"09","article_processing_charge":"No","publication_identifier":{"isbn":["9780470034590","9780470058213"]},"date_created":"2020-09-18T10:07:45Z","date_updated":"2021-01-12T08:19:24Z","volume":4,"oa_version":"None","author":[{"first_name":"Peixiang","last_name":"Ma","full_name":"Ma, Peixiang"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"}],"publication_status":"published","title":"Conformational exchange processes in biological systems: Detection by solid-state NMR","status":"public","intvolume":" 4","publisher":"Wiley","_id":"8457","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","extern":"1","abstract":[{"text":"We review recent advances in methodologies to study microseconds‐to‐milliseconds exchange processes in biological molecules using magic‐angle spinning solid‐state nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations and experimental data. These simulations reveal the potential of MAS NMR to provide detailed insight into short‐lived conformations of biological molecules. Recent studies of conformational exchange dynamics in microcrystalline ubiquitin are discussed.","lang":"eng"}],"issue":"3","type":"journal_article"},{"intvolume":" 32","publisher":"Oxford University Press","status":"public","publication_status":"published","title":"A model of substitution trajectories in sequence space and long-term protein evolution","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"848","year":"2015","oa_version":"None","volume":32,"date_updated":"2021-01-12T08:19:33Z","date_created":"2018-12-11T11:48:49Z","author":[{"full_name":"Usmanova, Dinara","last_name":"Usmanova","first_name":"Dinara"},{"first_name":"Luca","last_name":"Ferretti","full_name":"Ferretti, Luca"},{"full_name":"Povolotskaya, Inna","last_name":"Povolotskaya","first_name":"Inna"},{"full_name":"Vlasov, Peter","first_name":"Peter","last_name":"Vlasov"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"}],"type":"journal_article","extern":"1","issue":"2","publist_id":"6804","abstract":[{"text":"The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.","lang":"eng"}],"page":"542 - 554","quality_controlled":"1","citation":{"short":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554.","mla":"Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318.","chicago":"Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/molbev/msu318.","ama":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318","apa":"Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov, F. (2015). A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu318","ieee":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015.","ista":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 32(2), 542–554."},"publication":"Molecular Biology and Evolution","language":[{"iso":"eng"}],"doi":"10.1093/molbev/msu318","date_published":"2015-02-01T00:00:00Z","day":"01","month":"02"},{"status":"public","title":"Arnold diffusion for smooth convex systems of two and a half degrees of freedom","publication_status":"published","publisher":"IOP Publishing","intvolume":" 28","_id":"8498","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:41Z","date_created":"2020-09-18T10:46:43Z","volume":28,"oa_version":"None","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim","last_name":"Kaloshin","full_name":"Kaloshin, Vadim"},{"full_name":"Zhang, K","first_name":"K","last_name":"Zhang"}],"type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"In the present note we announce a proof of a strong form of Arnold diffusion for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$ be a 2-dimensional torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ > 0. Our main result says that for a 'generic' time-periodic perturbation of an integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad \\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur proof is a combination of geometric and variational methods. The fundamental elements of the construction are the usage of crumpled normally hyperbolic invariant cylinders from [9], flower and simple normally hyperbolic invariant manifolds from [36] as well as their kissing property at a strong double resonance. This allows us to build a 'connected' net of three-dimensional normally hyperbolic invariant manifolds. To construct diffusing orbits along this net we employ a version of the Mather variational method [41] equipped with weak KAM theory [28], proposed by Bernard in [7]."}],"issue":"8","article_type":"original","quality_controlled":"1","page":"2699-2720","publication":"Nonlinearity","citation":{"ama":"Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 2015;28(8):2699-2720. doi:10.1088/0951-7715/28/8/2699","ista":"Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720.","apa":"Kaloshin, V., & Zhang, K. (2015). Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. IOP Publishing. https://doi.org/10.1088/0951-7715/28/8/2699","ieee":"V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two and a half degrees of freedom,” Nonlinearity, vol. 28, no. 8. IOP Publishing, pp. 2699–2720, 2015.","mla":"Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity, vol. 28, no. 8, IOP Publishing, 2015, pp. 2699–720, doi:10.1088/0951-7715/28/8/2699.","short":"V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720.","chicago":"Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity. IOP Publishing, 2015. https://doi.org/10.1088/0951-7715/28/8/2699."},"language":[{"iso":"eng"}],"date_published":"2015-06-30T00:00:00Z","doi":"10.1088/0951-7715/28/8/2699","keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"month":"06","day":"30","article_processing_charge":"No","publication_identifier":{"issn":["0951-7715","1361-6544"]}},{"page":"71-149","quality_controlled":"1","article_type":"original","citation":{"ista":"Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 17(1), 71–149.","apa":"Guardia, M., & Kaloshin, V. (2015). Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. European Mathematical Society Publishing House. https://doi.org/10.4171/jems/499","ieee":"M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation,” Journal of the European Mathematical Society, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015.","ama":"Guardia M, Kaloshin V. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 2015;17(1):71-149. doi:10.4171/jems/499","chicago":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical Society. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/jems/499.","mla":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical Society, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 71–149, doi:10.4171/jems/499.","short":"M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17 (2015) 71–149."},"publication":"Journal of the European Mathematical Society","language":[{"iso":"eng"}],"doi":"10.4171/jems/499","date_published":"2015-02-05T00:00:00Z","publication_identifier":{"issn":["1435-9855"]},"article_processing_charge":"No","day":"05","month":"02","publisher":"European Mathematical Society Publishing House","intvolume":" 17","title":"Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation","status":"public","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8499","year":"2015","volume":17,"oa_version":"None","date_updated":"2021-01-12T08:19:41Z","date_created":"2020-09-18T10:46:50Z","author":[{"first_name":"Marcel","last_name":"Guardia","full_name":"Guardia, Marcel"},{"last_name":"Kaloshin","first_name":"Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim"}],"type":"journal_article","extern":"1","issue":"1","abstract":[{"lang":"eng","text":"We consider the cubic defocusing nonlinear Schrödinger equation in the two dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe establish the existence of solutions with polynomial time estimates. More exactly, there is c>0 such that for any K≫1 we find a solution u and a time T such that ∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0et al., “Artificial rheotaxis,” Science Advances, vol. 1, no. 4. American Association for the Advancement of Science , 2015.","apa":"Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances. American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214","ama":"Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science Advances. 2015;1(4). doi:10.1126/sciadv.1400214","chicago":"Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” Science Advances. American Association for the Advancement of Science , 2015. https://doi.org/10.1126/sciadv.1400214.","mla":"Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:10.1126/sciadv.1400214.","short":"J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg, D.J. Pine, P.M. Chaikin, Science Advances 1 (2015)."},"publication":"Science Advances","article_type":"original"},{"day":"11","month":"05","doi":"10.1371/journal.pone.0125888","date_published":"2015-05-11T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888","ista":"Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).","ieee":"O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","apa":"Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0125888","mla":"Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.","short":"O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015).","chicago":"Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888."},"publication":"PLoS One","quality_controlled":0,"publist_id":"6742","issue":"5","abstract":[{"lang":"eng","text":"The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1."}],"extern":1,"type":"journal_article","author":[{"full_name":"Arkhipova, Oksana V","last_name":"Arkhipova","first_name":"Oksana"},{"full_name":"Meer, Margarita V","last_name":"Meer","first_name":"Margarita"},{"full_name":"Mikoulinskaia, Galina V","first_name":"Galina","last_name":"Mikoulinskaia"},{"first_name":"Marina","last_name":"Zakharova","full_name":"Zakharova, Marina V"},{"full_name":"Galushko, Alexander S","first_name":"Alexander","last_name":"Galushko"},{"last_name":"Akimenko","first_name":"Vasilii","full_name":"Akimenko, Vasilii K"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov"}],"volume":10,"date_updated":"2021-01-12T08:21:48Z","date_created":"2018-12-11T11:49:08Z","acknowledgement":"Funding: The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, \"Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)\" and (BFU2012-31329), the European Union and the European Research Council under grant agreement 335980_EinME. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Our author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher until last days. A number of his work remains unfinished. We mourn premature care of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for the sequencing.","_id":"906","year":"2015","intvolume":" 10","publisher":"Public Library of Science","status":"public","publication_status":"published","title":"Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer"},{"publication":"Journal of Geophysical Research: Oceans","citation":{"mla":"Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.","short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.","chicago":"Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598.","ama":"Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777. doi:10.1002/2014jc010598","ista":"Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.","apa":"Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2014jc010598","ieee":"A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” Journal of Geophysical Research: Oceans, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015."},"article_type":"original","page":"4760-4777","date_published":"2015-06-08T00:00:00Z","day":"08","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9141","status":"public","title":"A three-dimensional map of tidal dissipation over abyssal hills","intvolume":" 120","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere."}],"issue":"7","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2014JC010598"}],"oa":1,"quality_controlled":"1","doi":"10.1002/2014jc010598","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["2169-9275"]},"year":"2015","publication_status":"published","publisher":"American Geophysical Union","author":[{"full_name":"Lefauve, Adrien","last_name":"Lefauve","first_name":"Adrien"},{"orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J","full_name":"Muller, Caroline J"},{"full_name":"Melet, Angélique","last_name":"Melet","first_name":"Angélique"}],"date_updated":"2022-01-24T13:45:41Z","date_created":"2021-02-15T14:21:49Z","volume":120,"extern":"1"},{"type":"journal_article","abstract":[{"text":"The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"928","ddc":["539","570"],"status":"public","title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","intvolume":" 4","oa_version":"Published Version","file":[{"file_id":"5769","relation":"main_file","checksum":"1e4024b3161adcae4a53a0b3dc8a946e","date_created":"2018-12-20T15:50:56Z","date_updated":"2020-07-14T12:48:15Z","access_level":"open_access","file_name":"2015_eLife_Sehring.pdf","creator":"dernst","content_type":"application/pdf","file_size":7202224}],"day":"21","has_accepted_license":"1","publication":"eLife","citation":{"mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications, 2015, doi:10.7554/eLife.09206.","short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015).","chicago":"Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/eLife.09206.","ama":"Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206","ista":"Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206.","apa":"Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206","ieee":"I. Sehring et al., “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences Publications, 2015."},"date_published":"2015-10-21T00:00:00Z","article_number":"e09206","file_date_updated":"2020-07-14T12:48:15Z","publist_id":"6512","extern":"1","year":"2015","publication_status":"published","publisher":"eLife Sciences Publications","author":[{"full_name":"Sehring, Ivonne","first_name":"Ivonne","last_name":"Sehring"},{"first_name":"Pierre","last_name":"Recho","full_name":"Recho, Pierre"},{"last_name":"Denker","first_name":"Elsa","full_name":"Denker, Elsa"},{"first_name":"Matthew","last_name":"Kourakis","full_name":"Kourakis, Matthew"},{"last_name":"Mathiesen","first_name":"Birthe","full_name":"Mathiesen, Birthe"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"Dong, Bo","first_name":"Bo","last_name":"Dong"},{"last_name":"Jiang","first_name":"Di","full_name":"Jiang, Di"}],"date_created":"2018-12-11T11:49:15Z","date_updated":"2021-01-12T08:21:58Z","volume":4,"month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.7554/eLife.09206","language":[{"iso":"eng"}]},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2015-11-01T00:00:00Z","citation":{"chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier, 2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187.","apa":"Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics, vol. 49. Elsevier, pp. 181–187, 2015.","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187. doi:10.1016/j.endm.2015.06.027"},"publication":"Electronic Notes in Discrete Mathematics","page":"181-187","article_type":"original","abstract":[{"text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"9575","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","intvolume":" 49","title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","status":"public","publication_identifier":{"issn":["1571-0653"]},"month":"11","doi":"10.1016/j.endm.2015.06.027","language":[{"iso":"eng"}],"external_id":{"arxiv":["1501.04816"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.04816"}],"oa":1,"quality_controlled":"1","extern":"1","author":[{"full_name":"Krivelevich, Michael","last_name":"Krivelevich","first_name":"Michael"},{"last_name":"Kwan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"},{"full_name":"Sudakov, Benny","last_name":"Sudakov","first_name":"Benny"}],"volume":49,"date_created":"2021-06-21T06:40:34Z","date_updated":"2023-02-23T14:01:28Z","year":"2015","publisher":"Elsevier","publication_status":"published"},{"_id":"9673","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","publisher":"Elsevier","intvolume":" 67","title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","status":"public","publication_status":"published","author":[{"first_name":"H.S.","last_name":"Leung","full_name":"Leung, H.S."},{"last_name":"Leung","first_name":"P.S.S.","full_name":"Leung, P.S.S."},{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"last_name":"Ngan","first_name":"A.H.W.","full_name":"Ngan, A.H.W."}],"volume":67,"oa_version":"None","date_created":"2021-07-15T14:09:32Z","date_updated":"2023-02-23T14:04:28Z","type":"journal_article","abstract":[{"lang":"eng","text":"Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation."}],"extern":"1","citation":{"mla":"Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity, vol. 67, Elsevier, 2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009.","short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25.","chicago":"Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity. Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009.","ama":"Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009","ista":"Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 67, 1–25.","apa":"Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009","ieee":"H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” International Journal of Plasticity, vol. 67. Elsevier, pp. 1–25, 2015."},"publication":"International Journal of Plasticity","page":"1-25","article_type":"original","date_published":"2015-04-01T00:00:00Z","doi":"10.1016/j.ijplas.2014.09.009","language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"issn":["0749-6419"]},"article_processing_charge":"No","day":"01","month":"04"},{"article_number":"180102","extern":"1","publication_status":"published","publisher":"American Physical Society","year":"2015","date_created":"2021-07-19T10:07:22Z","date_updated":"2021-08-09T12:38:49Z","volume":92,"author":[{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing"},{"full_name":"Tribello, Gareth A.","last_name":"Tribello","first_name":"Gareth A."},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"month":"11","publication_identifier":{"eissn":["1550-235X"],"issn":["1098-0121"]},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1511.08668","open_access":"1"}],"external_id":{"arxiv":["1511.08668"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.92.180102","type":"journal_article","abstract":[{"lang":"eng","text":"The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification."}],"issue":"18","status":"public","title":"Solid-liquid interfacial free energy out of equilibrium","intvolume":" 92","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9688","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","publication":"Physical Review B - Condensed Matter and Materials Physics","citation":{"chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102.","short":"B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015).","mla":"Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102.","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18. American Physical Society, 2015.","apa":"Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102","ista":"Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 92(18), 180102.","ama":"Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 2015;92(18). doi:10.1103/physrevb.92.180102"},"date_published":"2015-11-01T00:00:00Z"},{"_id":"9711","year":"2015","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Excel file containing the raw data for all figures","department":[{"_id":"ToBo"}],"publisher":"Public Library of Science","author":[{"id":"424D78A0-F248-11E8-B48F-1D18A9856A87","last_name":"Chevereau","first_name":"Guillaume","full_name":"Chevereau, Guillaume"},{"first_name":"Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","full_name":"Lukacisinova, Marta"},{"full_name":"Batur, Tugce","first_name":"Tugce","last_name":"Batur"},{"last_name":"Guvenek","first_name":"Aysegul","full_name":"Guvenek, Aysegul"},{"last_name":"Ayhan","first_name":"Dilay Hazal","full_name":"Ayhan, Dilay Hazal"},{"full_name":"Toprak, Erdal","first_name":"Erdal","last_name":"Toprak"},{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"1619","relation":"used_in_publication","status":"public"}]},"date_created":"2021-07-23T11:53:50Z","date_updated":"2023-02-23T10:07:02Z","oa_version":"Published Version","type":"research_data_reference","citation":{"short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","mla":"Chevereau, Guillaume, et al. Excel File Containing the Raw Data for All Figures. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s001.","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing the Raw Data for All Figures.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s001.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw data for all figures. 2015. doi:10.1371/journal.pbio.1002299.s001","ieee":"G. Chevereau et al., “Excel file containing the raw data for all figures.” Public Library of Science, 2015.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Excel file containing the raw data for all figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s001","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Excel file containing the raw data for all figures, Public Library of Science, 10.1371/journal.pbio.1002299.s001."},"doi":"10.1371/journal.pbio.1002299.s001","date_published":"2015-11-18T00:00:00Z","day":"18","month":"11","article_processing_charge":"No"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"03","page":"615 - 624","article_type":"original","citation":{"ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 2015;84(3):615-624. doi:10.1111/1365-2656.12345","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2015. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 84(3), 615–624.","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees,” Journal of Animal Ecology, vol. 84, no. 3. Wiley, pp. 615–624, 2015.","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton, R. (2015). A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12345","mla":"Mcmahon, Dino, et al. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology, vol. 84, no. 3, Wiley, 2015, pp. 615–24, doi:10.1111/1365-2656.12345.","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal of Animal Ecology 84 (2015) 615–624.","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology. Wiley, 2015. https://doi.org/10.1111/1365-2656.12345."},"publication":"Journal of Animal Ecology","date_published":"2015-03-03T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline."}],"intvolume":" 84","ddc":["570"],"status":"public","title":"A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees","_id":"1855","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","file":[{"file_name":"IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1823045,"creator":"system","relation":"main_file","file_id":"5350","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:18:29Z","checksum":"542a0b9b07e78050a81b35f26f0b82da"}],"pubrep_id":"460","month":"03","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["25646973"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/1365-2656.12345","publist_id":"5245","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"SyCr"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2015","acknowledgement":"We thank J.R. de Miranda, L. De Smet and D. de Graaf for supplying qRT-PCR and MLPA positive controls, respectively, in the form of plasmids. This work was supported by the Insect Pollinators Initiative (IPI grants BB/1000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, The Scottish Government and The Wellcome Trust, under the Living with Environmental Change Partnership.","volume":84,"date_updated":"2023-02-23T14:06:09Z","date_created":"2018-12-11T11:54:23Z","related_material":{"record":[{"id":"9720","status":"public","relation":"research_data"}]},"author":[{"full_name":"Mcmahon, Dino","first_name":"Dino","last_name":"Mcmahon"},{"full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","first_name":"Matthias"},{"full_name":"Caspar, Jesicca","first_name":"Jesicca","last_name":"Caspar"},{"first_name":"Panagiotis","last_name":"Theodorou","full_name":"Theodorou, Panagiotis"},{"last_name":"Brown","first_name":"Mark","full_name":"Brown, Mark"},{"full_name":"Paxton, Robert","first_name":"Robert","last_name":"Paxton"}]},{"oa_version":"Submitted Version","intvolume":" 370","status":"public","title":"Opposing effects of allogrooming on disease transmission in ant societies","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"1830","issue":"1669","abstract":[{"lang":"eng","text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems."}],"type":"journal_article","date_published":"2015-05-26T00:00:00Z","article_type":"original","citation":{"chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2015. https://doi.org/10.1098/rstb.2014.0108.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","mla":"Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, Royal Society, The, 2015, doi:10.1098/rstb.2014.0108.","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2014.0108","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming on disease transmission in ant societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, The, 2015.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669).","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0108"},"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","article_processing_charge":"No","day":"26","scopus_import":"1","volume":370,"date_updated":"2023-02-23T14:06:12Z","date_created":"2018-12-11T11:54:15Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9721"}]},"author":[{"full_name":"Theis, Fabian","first_name":"Fabian","last_name":"Theis"},{"last_name":"Ugelvig","first_name":"Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V"},{"first_name":"Carsten","last_name":"Marr","full_name":"Marr, Carsten"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"publisher":"Royal Society, The","department":[{"_id":"SyCr"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Meghan L. Vyleta for the genetical fungal strain characterization and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D. Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments on the manuscript.","year":"2015","ec_funded":1,"publist_id":"5273","language":[{"iso":"eng"}],"doi":"10.1098/rstb.2014.0108","project":[{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7"},{"grant_number":"302004","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","call_identifier":"FP7"},{"name":"Antnet","_id":"25E0E184-B435-11E9-9278-68D0E5697425"},{"name":"Fellowship of Wissenschaftskolleg zu Berlin","_id":"25E24DB2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/"}],"external_id":{"pmid":["25870394"]},"oa":1,"publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"month":"05"},{"citation":{"ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming on disease transmission in ant societies. 2015. doi:10.5061/dryad.dj2bf","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Data from: Opposing effects of allogrooming on disease transmission in ant societies. Dryad. https://doi.org/10.5061/dryad.dj2bf","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects of allogrooming on disease transmission in ant societies.” Dryad, 2015.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects of allogrooming on disease transmission in ant societies, Dryad, 10.5061/dryad.dj2bf.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).","mla":"Theis, Fabian, et al. Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies. Dryad, 2015, doi:10.5061/dryad.dj2bf.","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Dryad, 2015. https://doi.org/10.5061/dryad.dj2bf."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.dj2bf","open_access":"1"}],"date_published":"2015-12-29T00:00:00Z","doi":"10.5061/dryad.dj2bf","month":"12","day":"29","article_processing_charge":"No","year":"2015","_id":"9721","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Data from: Opposing effects of allogrooming on disease transmission in ant societies","department":[{"_id":"SyCr"}],"publisher":"Dryad","author":[{"full_name":"Theis, Fabian","first_name":"Fabian","last_name":"Theis"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","first_name":"Line V","last_name":"Ugelvig","full_name":"Ugelvig, Line V"},{"first_name":"Carsten","last_name":"Marr","full_name":"Marr, Carsten"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1830"}]},"date_created":"2021-07-26T09:38:36Z","date_updated":"2023-02-23T10:16:22Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.","lang":"eng"}]},{"title":"Supporting information text","status":"public","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","_id":"9718","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","date_created":"2021-07-26T08:35:23Z","date_updated":"2023-02-23T10:16:13Z","oa_version":"Published Version","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","first_name":"Tamar","full_name":"Friedlander, Tamar"},{"last_name":"Mayo","first_name":"Avraham E.","full_name":"Mayo, Avraham E."},{"full_name":"Tlusty, Tsvi","last_name":"Tlusty","first_name":"Tsvi"},{"first_name":"Uri","last_name":"Alon","full_name":"Alon, Uri"}],"related_material":{"record":[{"id":"1827","relation":"used_in_publication","status":"public"}]},"type":"research_data_reference","citation":{"short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","mla":"Friedlander, Tamar, et al. Supporting Information Text. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001.","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s001.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:10.1371/journal.pcbi.1004055.s001","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Supporting information text. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s001","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, 10.1371/journal.pcbi.1004055.s001."},"date_published":"2015-03-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004055.s001","month":"03","day":"23","article_processing_charge":"No"},{"type":"journal_article","issue":"6","abstract":[{"text":"We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth.","lang":"eng"}],"intvolume":" 10","status":"public","title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","ddc":["000"],"_id":"1793","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf","creator":"system","content_type":"application/pdf","file_size":1850825,"file_id":"5150","relation":"main_file","checksum":"d20f26461ca575276ad3ed9ce4bfc787","date_created":"2018-12-12T10:15:30Z","date_updated":"2020-07-14T12:45:16Z"}],"oa_version":"Published Version","pubrep_id":"454","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.","short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).","mla":"Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One, vol. 10, no. 6, e0127657, Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots,” PLoS One, vol. 10, no. 6. Public Library of Science, 2015.","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. 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Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:10.1371/journal.pone.0127657.s001","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015.","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657.s001","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, 10.1371/journal.pone.0127657.s001.","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015).","mla":"Symonova, Olga, et al. Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2. Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.s001.","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.s001."}},{"month":"03","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1004055","file_date_updated":"2020-07-14T12:45:17Z","publist_id":"5278","ec_funded":1,"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","year":"2015","date_updated":"2023-02-23T14:07:51Z","date_created":"2018-12-11T11:54:14Z","volume":11,"author":[{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mayo, Avraham","last_name":"Mayo","first_name":"Avraham"},{"full_name":"Tlusty, Tsvi","first_name":"Tsvi","last_name":"Tlusty"},{"first_name":"Uri","last_name":"Alon","full_name":"Alon, Uri"}],"related_material":{"record":[{"id":"9718","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9773"}]},"scopus_import":1,"day":"23","has_accepted_license":"1","article_processing_charge":"No","publication":"PLoS Computational Biology","citation":{"ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).","apa":"Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of bow-tie architectures in biology. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055","ieee":"T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015.","ama":"Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055","chicago":"Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.","mla":"Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.","short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015)."},"date_published":"2015-03-23T00:00:00Z","type":"journal_article","abstract":[{"text":"Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.","lang":"eng"}],"issue":"3","status":"public","ddc":["576"],"title":"Evolution of bow-tie architectures in biology","intvolume":" 11","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1827","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5161","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:15:39Z","checksum":"b8aa66f450ff8de393014b87ec7d2efb","file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf","access_level":"open_access","file_size":1811647,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"452"},{"publication":"PLoS One","citation":{"ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907","ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907."},"date_published":"2015-05-18T00:00:00Z","scopus_import":1,"day":"18","has_accepted_license":"1","_id":"1809","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Indirect genetic effects and the dynamics of social interactions","status":"public","ddc":["570","576"],"intvolume":" 10","pubrep_id":"453","file":[{"checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","date_created":"2018-12-12T10:09:07Z","date_updated":"2020-07-14T12:45:17Z","file_id":"4730","relation":"main_file","creator":"system","file_size":2748982,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations."}],"issue":"5","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pone.0126907","language":[{"iso":"eng"}],"month":"05","year":"2015","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"author":[{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova","full_name":"Trubenova, Barbora"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9715"},{"relation":"research_data","status":"public","id":"9772"}]},"date_updated":"2023-02-23T14:07:48Z","date_created":"2018-12-11T11:54:07Z","volume":10,"file_date_updated":"2020-07-14T12:45:17Z","publist_id":"5299"},{"month":"05","day":"18","article_processing_charge":"No","citation":{"chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","mla":"Trubenova, Barbora, et al. Description of the Agent Based Simulations. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, 10.1371/journal.pone.0126907.s003.","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:10.1371/journal.pone.0126907.s003"},"date_published":"2015-05-18T00:00:00Z","doi":"10.1371/journal.pone.0126907.s003","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9772","year":"2015","title":"Description of the agent based simulations","status":"public","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","author":[{"full_name":"Trubenova, Barbora","last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1809"}]},"date_created":"2021-08-05T12:55:20Z","date_updated":"2023-02-23T10:15:25Z","oa_version":"Published Version"},{"citation":{"chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","mla":"Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002.","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, 10.1371/journal.pcbi.1004055.s002.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:10.1371/journal.pcbi.1004055.s002"},"doi":"10.1371/journal.pcbi.1004055.s002","date_published":"2015-03-23T00:00:00Z","month":"03","day":"23","article_processing_charge":"No","_id":"9773","year":"2015","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Evolutionary simulation code","status":"public","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"author":[{"first_name":"Tamar","last_name":"Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar"},{"last_name":"Mayo","first_name":"Avraham E.","full_name":"Mayo, Avraham E."},{"full_name":"Tlusty, Tsvi","last_name":"Tlusty","first_name":"Tsvi"},{"last_name":"Alon","first_name":"Uri","full_name":"Alon, Uri"}],"related_material":{"record":[{"id":"1827","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-05T12:58:07Z","date_updated":"2023-02-23T10:16:13Z","oa_version":"Published Version","type":"research_data_reference"},{"date_updated":"2021-01-12T08:22:24Z","date_created":"2018-12-11T11:49:31Z","volume":14,"author":[{"first_name":"Ilija","last_name":"Zeljkovic","full_name":"Zeljkovic, Ilija"},{"first_name":"Yoshinori","last_name":"Okada","full_name":"Okada, Yoshinori"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Maksym Serbyn"},{"first_name":"Raman","last_name":"Sankar","full_name":"Sankar, Raman"},{"full_name":"Walkup, Daniel","first_name":"Daniel","last_name":"Walkup"},{"first_name":"Wenwen","last_name":"Zhou","full_name":"Zhou, Wenwen"},{"last_name":"Liu","first_name":"Junwei","full_name":"Liu, Junwei"},{"full_name":"Chang, Guoqing","last_name":"Chang","first_name":"Guoqing"},{"full_name":"Wang, Yungjui","first_name":"Yungjui","last_name":"Wang"},{"first_name":"Md","last_name":"Hasan","full_name":"Hasan, Md Z"},{"full_name":"Chou, Fangcheng","first_name":"Fangcheng","last_name":"Chou"},{"full_name":"Lin, Hsin","last_name":"Lin","first_name":"Hsin"},{"full_name":"Bansil, Arun","first_name":"Arun","last_name":"Bansil"},{"full_name":"Fu, Liang","first_name":"Liang","last_name":"Fu"},{"full_name":"Madhavan, Vidya","first_name":"Vidya","last_name":"Madhavan"}],"publication_status":"published","status":"public","title":"Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators","publisher":"Nature Publishing Group","intvolume":" 14","_id":"981","year":"2015","acknowledgement":"We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny, A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon for help with EDS measurements. V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004.","extern":1,"abstract":[{"lang":"eng","text":"The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials."}],"issue":"3","publist_id":"6419","type":"journal_article","doi":"10.1038/nmat4215","date_published":"2015-03-01T00:00:00Z","quality_controlled":0,"page":"318 - 324","publication":"Nature Materials","oa":1,"citation":{"chicago":"Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials. Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215.","short":"I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu, G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature Materials 14 (2015) 318–324.","mla":"Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials, vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215.","apa":"Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. Nature Publishing Group. https://doi.org/10.1038/nmat4215","ieee":"I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators,” Nature Materials, vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.","ista":"Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G, Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 14(3), 318–324.","ama":"Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 2015;14(3):318-324. doi:10.1038/nmat4215"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.4906"}],"month":"03","day":"01"},{"author":[{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry A"}],"volume":5,"date_created":"2018-12-11T11:49:32Z","date_updated":"2021-01-12T08:22:25Z","_id":"982","year":"2015","acknowledgement":"We acknowledge helpful discussions with Sid Parameswaran, Andrew Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor library. Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. This research was supported by Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation, NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities of Leeds and Manchester.","intvolume":" 5","publisher":"American Physical Society","status":"public","title":"Criterion for many-body localization-delocalization phase transition","publication_status":"published","issue":"4","publist_id":"6418","abstract":[{"text":"We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions.","lang":"eng"}],"extern":1,"type":"journal_article","doi":"10.1103/PhysRevX.5.041047","date_published":"2015-01-01T00:00:00Z","citation":{"chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X. American Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047.","mla":"Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical Society, 2015, doi:10.1103/PhysRevX.5.041047.","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).","ista":"Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization phase transition. Physical Review X. 5(4).","apa":"Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization phase transition,” Physical Review X, vol. 5, no. 4. American Physical Society, 2015.","ama":"Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047"},"main_file_link":[{"url":"https://arxiv.org/abs/1507.01635","open_access":"1"}],"oa":1,"publication":"Physical Review X","quality_controlled":0,"day":"01","month":"01"},{"publist_id":"7955","extern":"1","acknowledgement":"Research support by Microsoft Project Q, the Danish National Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M. acknowledges support from the Villum Foundation.","year":"2015","publication_status":"published","publisher":"Nature Publishing Group","author":[{"orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"},{"full_name":"Albrecht, S M","last_name":"Albrecht","first_name":"S M"},{"last_name":"Kiršanskas","first_name":"Gediminas","full_name":"Kiršanskas, Gediminas"},{"last_name":"Chang","first_name":"W","full_name":"Chang, W"},{"full_name":"Kuemmeth, Ferdinand","last_name":"Kuemmeth","first_name":"Ferdinand"},{"full_name":"Krogstrup, Peter","last_name":"Krogstrup","first_name":"Peter"},{"last_name":"Jespersen","first_name":"Thomas","full_name":"Jespersen, Thomas"},{"first_name":"Jesper","last_name":"Nygård","full_name":"Nygård, Jesper"},{"first_name":"Karsten","last_name":"Flensberg","full_name":"Flensberg, Karsten"},{"full_name":"Marcus, Charles","first_name":"Charles","last_name":"Marcus"}],"date_updated":"2021-01-12T08:22:28Z","date_created":"2018-12-11T11:44:37Z","volume":11,"month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.05155"}],"external_id":{"arxiv":["1501.05155"]},"oa":1,"quality_controlled":"1","doi":"10.1038/nphys3461","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms.","lang":"eng"}],"issue":"12","_id":"99","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Parity lifetime of bound states in a proximitized semiconductor nanowire","status":"public","intvolume":" 11","oa_version":"Preprint","day":"14","publication":"Nature Physics","citation":{"chicago":"Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg, and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3461.","short":"A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P. Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11 (2015) 1017–1021.","mla":"Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 1017–21, doi:10.1038/nphys3461.","ieee":"A. P. Higginbotham et al., “Parity lifetime of bound states in a proximitized semiconductor nanowire,” Nature Physics, vol. 11, no. 12. Nature Publishing Group, pp. 1017–1021, 2015.","apa":"Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth, F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3461","ista":"Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021.","ama":"Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 2015;11(12):1017-1021. doi:10.1038/nphys3461"},"page":"1017 - 1021","date_published":"2015-09-14T00:00:00Z"},{"volume":144,"oa_version":"None","date_updated":"2021-01-12T08:19:40Z","date_created":"2020-09-18T10:46:14Z","author":[{"first_name":"Abed","last_name":"Bounemoura","full_name":"Bounemoura, Abed"},{"last_name":"Kaloshin","first_name":"Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim"}],"publisher":"American Mathematical Society","intvolume":" 144","title":"A note on micro-instability for Hamiltonian systems close to integrable","status":"public","publication_status":"published","_id":"8495","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","issue":"4","abstract":[{"text":"In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \\sqrt {\\varepsilon }$, after a time of order $ \\sqrt {\\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1090/proc/12796","date_published":"2015-12-21T00:00:00Z","page":"1553-1560","article_type":"letter_note","quality_controlled":"1","citation":{"chicago":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796.","mla":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796.","short":"A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society 144 (2015) 1553–1560.","ista":"Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 144(4), 1553–1560.","apa":"Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12796","ieee":"A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian systems close to integrable,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.","ama":"Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 2015;144(4):1553-1560. doi:10.1090/proc/12796"},"publication":"Proceedings of the American Mathematical Society","article_processing_charge":"No","publication_identifier":{"issn":["0002-9939","1088-6826"]},"day":"21","month":"12"},{"issue":"30","publist_id":"6783","abstract":[{"lang":"eng","text":"Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF."}],"extern":1,"type":"journal_article","author":[{"full_name":"Kretz, Colin A","last_name":"Kretz","first_name":"Colin"},{"full_name":"Dai, Manhong","last_name":"Dai","first_name":"Manhong"},{"first_name":"Onuralp","last_name":"Soylemez","full_name":"Soylemez, Onuralp"},{"full_name":"Yee, Andrew","last_name":"Yee","first_name":"Andrew"},{"first_name":"Karl","last_name":"Desch","full_name":"Desch, Karl C"},{"last_name":"Siemieniak","first_name":"David","full_name":"Siemieniak, David R"},{"full_name":"Tomberg, Kärt","first_name":"Kärt","last_name":"Tomberg"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov"},{"last_name":"Meng","first_name":"Fan","full_name":"Meng, Fan"},{"full_name":"Ginsburg, David B","last_name":"Ginsburg","first_name":"David"}],"volume":112,"date_created":"2018-12-11T11:48:55Z","date_updated":"2021-01-12T08:20:26Z","_id":"866","acknowledgement":"We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.\n","year":"2015","publisher":"National Academy of Sciences","intvolume":" 112","title":"Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13","publication_status":"published","status":"public","month":"07","day":"28","doi":"10.1073/pnas.1511328112","date_published":"2015-07-28T00:00:00Z","citation":{"ama":"Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 2015;112(30):9328-9333. doi:10.1073/pnas.1511328112","ista":"Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.","apa":"Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511328112","ieee":"C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015.","mla":"Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112.","short":"C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.","chicago":"Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112."},"publication":"PNAS","page":"9328 - 9333","quality_controlled":0},{"abstract":[{"text":"The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space.","lang":"eng"}],"publist_id":"6764","issue":"1","extern":1,"type":"journal_article","author":[{"full_name":"Kondrashov, Dmitry A","last_name":"Kondrashov","first_name":"Dmitry"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov"}],"date_updated":"2021-01-12T08:21:16Z","date_created":"2018-12-11T11:49:01Z","volume":31,"_id":"886","year":"2015","acknowledgement":"This work has been supported by a grant from the HHMI International Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional Development Fund (ERDF), the European Union, and the European Research Council under grant agreement no 335980_EinME.","publication_status":"published","status":"public","title":"Topological features of rugged fitness landscapes in sequence space","intvolume":" 31","publisher":"Elsevier","day":"01","month":"01","doi":"10.1016/j.tig.2014.09.009","date_published":"2015-01-01T00:00:00Z","publication":"Trends in Genetics","citation":{"ieee":"D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33, 2015.","apa":"Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009","ista":"Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33.","ama":"Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009","chicago":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015. https://doi.org/10.1016/j.tig.2014.09.009.","short":"D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.","mla":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009."},"quality_controlled":0,"page":"24 - 33"},{"extern":"1","volume":43,"date_updated":"2023-02-23T13:46:50Z","date_created":"2021-01-19T11:01:01Z","author":[{"first_name":"Nicolas","last_name":"Richet","full_name":"Richet, Nicolas"},{"full_name":"Liu, Danni","first_name":"Danni","last_name":"Liu"},{"first_name":"Pierre","last_name":"Legrand","full_name":"Legrand, Pierre"},{"full_name":"Velours, Christophe","first_name":"Christophe","last_name":"Velours"},{"first_name":"Armelle","last_name":"Corpet","full_name":"Corpet, Armelle"},{"last_name":"Gaubert","first_name":"Albane","full_name":"Gaubert, Albane"},{"last_name":"Bakail","first_name":"May M","orcid":"0000-0002-9592-1587","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","full_name":"Bakail, May M"},{"full_name":"Moal-Raisin, Gwenaelle","first_name":"Gwenaelle","last_name":"Moal-Raisin"},{"first_name":"Raphael","last_name":"Guerois","full_name":"Guerois, Raphael"},{"full_name":"Compper, Christel","last_name":"Compper","first_name":"Christel"},{"full_name":"Besle, Arthur","first_name":"Arthur","last_name":"Besle"},{"full_name":"Guichard, Berengère","first_name":"Berengère","last_name":"Guichard"},{"first_name":"Genevieve","last_name":"Almouzni","full_name":"Almouzni, Genevieve"},{"full_name":"Ochsenbein, Françoise","first_name":"Françoise","last_name":"Ochsenbein"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2015","publication_identifier":{"issn":["1362-4962","0305-1048"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1093/nar/gkv021","quality_controlled":"1","external_id":{"pmid":["25618846"]},"issue":"3","abstract":[{"text":"MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 43","title":"Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork","status":"public","_id":"9017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"18","date_published":"2015-02-18T00:00:00Z","page":"1905-1917","article_type":"original","citation":{"chicago":"Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv021.","short":"N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail, G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F. Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917.","mla":"Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research, vol. 43, no. 3, Oxford University Press, 2015, pp. 1905–17, doi:10.1093/nar/gkv021.","apa":"Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein, F. (2015). Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv021","ieee":"N. Richet et al., “Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork,” Nucleic Acids Research, vol. 43, no. 3. Oxford University Press, pp. 1905–1917, 2015.","ista":"Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 43(3), 1905–1917.","ama":"Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 2015;43(3):1905-1917. doi:10.1093/nar/gkv021"},"publication":"Nucleic Acids Research"},{"author":[{"full_name":"Boubaker, Riadh","first_name":"Riadh","last_name":"Boubaker"},{"full_name":"Platel, Vincent","first_name":"Vincent","last_name":"Platel"},{"first_name":"Alexis","last_name":"Bergès","full_name":"Bergès, Alexis"},{"full_name":"Bancelin, Mathieu","last_name":"Bancelin","first_name":"Mathieu"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"oa_version":"None","volume":76,"date_created":"2018-12-11T11:49:13Z","date_updated":"2021-01-12T08:21:56Z","_id":"924","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099).","intvolume":" 76","publisher":"Elsevier","publication_status":"published","status":"public","title":"Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop","publist_id":"6514","abstract":[{"lang":"eng","text":"This paper presents a numerical study of a Capillary Pumped Loop evaporator. A two-dimensional unsteady mathematical model of a flat evaporator is developed to simulate heat and mass transfer in unsaturated porous wick with phase change. The liquid-vapor phase change inside the porous wick is described by Langmuir's law. The governing equations are solved by the Finite Element Method. The results are presented then for a sintered nickel wick and methanol as a working fluid. The heat flux required to the transition from the all-liquid wick to the vapor-liquid wick is calculated. The dynamic and thermodynamic behavior of the working fluid in the capillary structure are discussed in this paper."}],"extern":"1","type":"journal_article","date_published":"2015-02-05T00:00:00Z","doi":"10.1016/j.applthermaleng.2014.10.009","language":[{"iso":"eng"}],"citation":{"mla":"Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol. 76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009.","short":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal Engineering 76 (2015) 1–8.","chicago":"Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering. Elsevier, 2015. https://doi.org/10.1016/j.applthermaleng.2014.10.009.","ama":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009","ista":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 76, 1–8.","apa":"Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015). Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009","ieee":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015."},"publication":"Applied Thermal Engineering","page":"1 - 8","article_processing_charge":"No","day":"05","month":"02"},{"extern":"1","issue":"28","publist_id":"6513","abstract":[{"lang":"eng","text":"An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. "}],"type":"journal_article","volume":112,"oa_version":"None","date_updated":"2021-01-12T08:21:59Z","date_created":"2018-12-11T11:49:15Z","author":[{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"full_name":"Dong, Bo","last_name":"Dong","first_name":"Bo"},{"full_name":"Recho, Pierre","first_name":"Pierre","last_name":"Recho"},{"last_name":"Joanny","first_name":"Jean","full_name":"Joanny, Jean"},{"full_name":"Hayashi, Shigeo","last_name":"Hayashi","first_name":"Shigeo"}],"intvolume":" 112","publisher":"National Academy of Sciences","status":"public","publication_status":"published","title":"Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes","_id":"929","acknowledgement":"We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro, Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto), and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions and discussion. This work was supported by the Taishan Scholar Program of Shandong and the Fundamental Research Funds for the Central Universities in China (3005000-841412019) (to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"14","month":"07","language":[{"iso":"eng"}],"date_published":"2015-07-14T00:00:00Z","doi":"10.1073/pnas.1504762112","page":"8620 - 8625","citation":{"ama":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 2015;112(28):8620-8625. doi:10.1073/pnas.1504762112","ista":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 112(28), 8620–8625.","apa":"Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015). Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112","ieee":"E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS, vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015.","mla":"Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112.","short":"E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.","chicago":"Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112."},"publication":"PNAS"},{"type":"journal_article","abstract":[{"text":"Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data.","lang":"eng"}],"issue":"50","_id":"933","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Physics of active jamming during collective cellular motion in a monolayer","status":"public","intvolume":" 112","oa_version":"None","day":"15","publication":"PNAS","citation":{"ama":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319. doi:10.1073/pnas.1510973112","apa":"García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112","ieee":"S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov, “Physics of active jamming during collective cellular motion in a monolayer,” PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015.","ista":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 112(50), 15314–15319.","short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","mla":"García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:10.1073/pnas.1510973112.","chicago":"García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan, and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112."},"page":"15314 - 15319","date_published":"2015-12-15T00:00:00Z","publist_id":"6511","extern":"1","year":"2015","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","author":[{"full_name":"García, Simón","first_name":"Simón","last_name":"García"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"last_name":"Elgeti","first_name":"Jens","full_name":"Elgeti, Jens"},{"full_name":"Joanny, Jean","last_name":"Joanny","first_name":"Jean"},{"first_name":"Pascal","last_name":"Silberzan","full_name":"Silberzan, Pascal"},{"full_name":"Gov, Nir","first_name":"Nir","last_name":"Gov"}],"date_updated":"2021-01-12T08:22:01Z","date_created":"2018-12-11T11:49:16Z","volume":112,"month":"12","main_file_link":[{"open_access":"1","url":"https://www.pnas.org/content/pnas/112/50/15314.full.pdf"}],"external_id":{"pmid":["26627719"]},"oa":1,"quality_controlled":"1","doi":"10.1073/pnas.1510973112","language":[{"iso":"eng"}]},{"publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"month":"12","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"pmid":["26680300"]},"language":[{"iso":"eng"}],"doi":"10.1101/gad.269902.115","extern":"1","file_date_updated":"2021-06-08T09:55:10Z","publisher":"Cold Spring Harbor Laboratory Press","department":[{"_id":"DaZi"}],"publication_status":"published","pmid":1,"year":"2015","volume":29,"date_updated":"2021-12-14T07:58:15Z","date_created":"2021-06-08T09:56:24Z","author":[{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"15","page":"2517–2531","article_type":"review","citation":{"ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","apa":"Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.269902.115","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115","chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531."},"publication":"Genes and Development","date_published":"2015-12-15T00:00:00Z","type":"journal_article","issue":"24","abstract":[{"text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.","lang":"eng"}],"intvolume":" 29","title":"Evolution and function of genomic imprinting in plants","ddc":["570"],"status":"public","_id":"9532","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"creator":"asandaue","content_type":"application/pdf","file_size":1116846,"file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","access_level":"open_access","date_created":"2021-06-08T09:55:10Z","date_updated":"2021-06-08T09:55:10Z","success":1,"checksum":"086a88cfca4677646da26ed960cb02e9","file_id":"9533","relation":"main_file"}]},{"publisher":"IOP Publishing","intvolume":" 23","status":"public","publication_status":"published","title":"Size dependence of yield strength simulated by a dislocation-density function dynamics approach","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9684","year":"2015","volume":23,"oa_version":"None","date_updated":"2023-02-23T14:04:54Z","date_created":"2021-07-19T09:11:12Z","author":[{"last_name":"Leung","first_name":"P S S","full_name":"Leung, P S S"},{"full_name":"Leung, H S","last_name":"Leung","first_name":"H S"},{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing"},{"full_name":"Ngan, A H W","last_name":"Ngan","first_name":"A H W"}],"type":"journal_article","article_number":"035001","extern":"1","issue":"3","abstract":[{"text":"The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept.","lang":"eng"}],"article_type":"original","quality_controlled":"1","citation":{"apa":"Leung, P. S. S., Leung, H. S., Cheng, B., & Ngan, A. H. W. (2015). Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. IOP Publishing. https://doi.org/10.1088/0965-0393/23/3/035001","ieee":"P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence of yield strength simulated by a dislocation-density function dynamics approach,” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3. IOP Publishing, 2015.","ista":"Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 23(3), 035001.","ama":"Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 2015;23(3). doi:10.1088/0965-0393/23/3/035001","chicago":"Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering. IOP Publishing, 2015. https://doi.org/10.1088/0965-0393/23/3/035001.","short":"P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015).","mla":"Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:10.1088/0965-0393/23/3/035001."},"publication":"Modelling and Simulation in Materials Science and Engineering","language":[{"iso":"eng"}],"date_published":"2015-04-01T00:00:00Z","doi":"10.1088/0965-0393/23/3/035001","scopus_import":"1","publication_identifier":{"eissn":["1361-651X"],"issn":["0965-0393"]},"article_processing_charge":"No","day":"01","month":"04"},{"publication":"PLoS Computational Biology","citation":{"mla":"Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004541.","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational Biology 11 (2015).","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541.","ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10). doi:10.1371/journal.pcbi.1004541","ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 11(10), e1004541.","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures,” PLoS Computational Biology, vol. 11, no. 10. Public Library of Science, 2015."},"date_published":"2015-10-23T00:00:00Z","scopus_import":1,"day":"23","has_accepted_license":"1","title":"An exploration of the universe of polyglutamine structures","status":"public","ddc":["570"],"intvolume":" 11","_id":"1566","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"5207","relation":"main_file","checksum":"8b67d729be663bfc9af04bfd94459655","date_created":"2018-12-12T10:16:21Z","date_updated":"2020-07-14T12:45:02Z","access_level":"open_access","file_name":"IST-2016-478-v1+1_journal.pcbi.1004541.pdf","creator":"system","content_type":"application/pdf","file_size":1412511}],"pubrep_id":"478","type":"journal_article","abstract":[{"text":"Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease.","lang":"eng"}],"issue":"10","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1004541","month":"10","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"CaHe"}],"acknowledgement":"We acknowledge the support by the EU Joint Programme in Neurodegenerative Diseases (JPND AC14/00037) project. The project is supported through the following funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland, National Science Centre; and Spain, ISCIII. ","year":"2015","date_created":"2018-12-11T11:52:45Z","date_updated":"2023-02-23T14:05:55Z","volume":11,"author":[{"full_name":"Gómez Sicilia, Àngel","first_name":"Àngel","last_name":"Gómez Sicilia"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","last_name":"Sikora","full_name":"Sikora, Mateusz K"},{"first_name":"Marek","last_name":"Cieplak","full_name":"Cieplak, Marek"},{"full_name":"Carrión Vázquez, Mariano","first_name":"Mariano","last_name":"Carrión Vázquez"}],"related_material":{"record":[{"id":"9714","relation":"research_data","status":"public"}]},"article_number":"e1004541","file_date_updated":"2020-07-14T12:45:02Z","publist_id":"5605"},{"month":"11","day":"06","article_processing_charge":"No","citation":{"ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness models for comparison & for interacting TFBSs. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639.s001","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison & for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison & for Interacting TFBSs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","mla":"Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001."},"date_published":"2015-11-06T00:00:00Z","doi":"10.1371/journal.pgen.1005639.s001","type":"research_data_reference","year":"2015","_id":"9712","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Other fitness models for comparison & for interacting TFBSs","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Public Library of Science","author":[{"last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"related_material":{"record":[{"id":"1666","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-02-23T10:09:08Z","date_created":"2021-07-23T12:00:37Z","oa_version":"Published Version"},{"type":"research_data_reference","_id":"9714","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","title":"An exploration of the universe of polyglutamine structures - submission to PLOS journals","status":"public","department":[{"_id":"CaHe"}],"publisher":"Public Library of Science ","author":[{"full_name":"Gómez Sicilia, Àngel","first_name":"Àngel","last_name":"Gómez Sicilia"},{"full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","first_name":"Mateusz K"},{"last_name":"Cieplak","first_name":"Marek","full_name":"Cieplak, Marek"},{"full_name":"Carrión Vázquez, Mariano","first_name":"Mariano","last_name":"Carrión Vázquez"}],"related_material":{"record":[{"id":"1566","relation":"used_in_publication","status":"public"}]},"date_updated":"2023-02-23T10:04:35Z","date_created":"2021-07-23T12:05:28Z","oa_version":"Published Version","month":"10","day":"23","article_processing_charge":"No","citation":{"ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures - submission to PLOS journals. 2015. doi:10.1371/journal.pcbi.1004541.s001","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures - submission to PLOS journals.” Public Library of Science , 2015.","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures - submission to PLOS journals. Public Library of Science . https://doi.org/10.1371/journal.pcbi.1004541.s001","ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures - submission to PLOS journals, Public Library of Science , 10.1371/journal.pcbi.1004541.s001.","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015).","mla":"Gómez Sicilia, Àngel, et al. An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals. Public Library of Science , 2015, doi:10.1371/journal.pcbi.1004541.s001.","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals.” Public Library of Science , 2015. https://doi.org/10.1371/journal.pcbi.1004541.s001."},"date_published":"2015-10-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004541.s001"},{"type":"research_data_reference","year":"2015","_id":"9715","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","title":"Mathematical inference of the results","status":"public","related_material":{"record":[{"id":"1809","status":"public","relation":"used_in_publication"}]},"author":[{"orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian","full_name":"Novak, Sebastian"},{"last_name":"Hager","first_name":"Reinmar","full_name":"Hager, Reinmar"}],"oa_version":"Published Version","date_created":"2021-07-23T12:11:30Z","date_updated":"2023-02-23T10:15:25Z","article_processing_charge":"No","month":"05","day":"18","citation":{"ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Mathematical inference of the results. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s001","ista":"Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, 10.1371/journal.pone.0126907.s001.","ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:10.1371/journal.pone.0126907.s001","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s001.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","mla":"Trubenova, Barbora, et al. Mathematical Inference of the Results. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001."},"doi":"10.1371/journal.pone.0126907.s001","date_published":"2015-05-18T00:00:00Z"},{"date_published":"2015-01-22T00:00:00Z","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","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.","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,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1799. The Royal Society, 2015.","apa":"Konrad, M., Grasse, A. V., 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. The Royal Society. https://doi.org/10.1098/rspb.2014.1976","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. 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. 2015;282(1799). doi:10.1098/rspb.2014.1976","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.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2014.1976.","mla":"Konrad, Matthias, et al. “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, vol. 282, no. 1799, 20141976, The Royal Society, 2015, doi:10.1098/rspb.2014.1976.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015)."},"article_type":"original","day":"22","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1993","status":"public","title":"Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","intvolume":" 282","abstract":[{"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. ","lang":"eng"}],"issue":"1799","type":"journal_article","doi":"10.1098/rspb.2014.1976","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/","open_access":"1"}],"external_id":{"pmid":["25473011"]},"quality_controlled":"1","project":[{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"}],"month":"01","publication_identifier":{"issn":["0962-8452"],"eissn":["1471-2954"]},"author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","first_name":"Matthias","full_name":"Konrad, Matthias"},{"full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tragust, Simon","first_name":"Simon","last_name":"Tragust","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"related_material":{"record":[{"id":"9740","status":"public","relation":"research_data"}]},"date_created":"2018-12-11T11:55:06Z","date_updated":"2023-02-23T14:06:41Z","volume":282,"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.","year":"2015","pmid":1,"publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"The Royal Society","ec_funded":1,"publist_id":"5090","article_number":"20141976"},{"department":[{"_id":"SyCr"}],"publisher":"Dryad","status":"public","title":"Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9742","year":"2015","oa_version":"Published Version","date_updated":"2023-02-23T10:30:52Z","date_created":"2021-07-28T08:52:53Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2161"}]},"author":[{"full_name":"Westhus, Claudia","first_name":"Claudia","last_name":"Westhus"},{"orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V","full_name":"Ugelvig, Line V"},{"full_name":"Tourdot, Edouard","last_name":"Tourdot","first_name":"Edouard"},{"last_name":"Heinze","first_name":"Jürgen","full_name":"Heinze, Jürgen"},{"full_name":"Doums, Claudie","first_name":"Claudie","last_name":"Doums"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"type":"research_data_reference","abstract":[{"text":"Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects.","lang":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.7kc79","open_access":"1"}],"citation":{"short":"C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015).","mla":"Westhus, Claudia, et al. Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant. Dryad, 2015, doi:10.5061/dryad.7kc79.","chicago":"Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Dryad, 2015. https://doi.org/10.5061/dryad.7kc79.","ama":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. 2015. doi:10.5061/dryad.7kc79","apa":"Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer, S. (2015). Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Dryad. https://doi.org/10.5061/dryad.7kc79","ieee":"C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant.” Dryad, 2015.","ista":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2015. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant, Dryad, 10.5061/dryad.7kc79."},"date_published":"2015-07-09T00:00:00Z","doi":"10.5061/dryad.7kc79","article_processing_charge":"No","day":"09","month":"07"},{"type":"research_data_reference","publisher":"Public Library of Science","department":[{"_id":"ToBo"}],"title":"Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs","status":"public","_id":"9765","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","oa_version":"Published Version","date_updated":"2023-02-23T10:07:02Z","date_created":"2021-08-03T07:05:16Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1619"}]},"author":[{"full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","last_name":"Chevereau","first_name":"Guillaume"},{"orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","first_name":"Marta","full_name":"Lukacisinova, Marta"},{"full_name":"Batur, Tugce","last_name":"Batur","first_name":"Tugce"},{"first_name":"Aysegul","last_name":"Guvenek","full_name":"Guvenek, Aysegul"},{"last_name":"Ayhan","first_name":"Dilay Hazal","full_name":"Ayhan, Dilay Hazal"},{"full_name":"Toprak, Erdal","first_name":"Erdal","last_name":"Toprak"},{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","month":"11","day":"18","citation":{"ama":"Chevereau G, Lukacisinova M, Batur T, et al. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. 2015. doi:10.1371/journal.pbio.1002299.s008","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs, Public Library of Science, 10.1371/journal.pbio.1002299.s008.","ieee":"G. Chevereau et al., “Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs.” Public Library of Science, 2015.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s008","mla":"Chevereau, Guillaume, et al. Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s008.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s008."},"doi":"10.1371/journal.pbio.1002299.s008","date_published":"2015-11-18T00:00:00Z"},{"author":[{"full_name":"Ragettli, S.","last_name":"Ragettli","first_name":"S."},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti"},{"full_name":"Immerzeel, W.W.","last_name":"Immerzeel","first_name":"W.W."},{"full_name":"Miles, E.S.","last_name":"Miles","first_name":"E.S."},{"first_name":"L.","last_name":"Petersen","full_name":"Petersen, L."},{"full_name":"Heynen, M.","last_name":"Heynen","first_name":"M."},{"full_name":"Shea, J.M.","first_name":"J.M.","last_name":"Shea"},{"first_name":"D.","last_name":"Stumm","full_name":"Stumm, D."},{"full_name":"Joshi, S.","first_name":"S.","last_name":"Joshi"},{"full_name":"Shrestha, A.","first_name":"A.","last_name":"Shrestha"}],"volume":78,"date_created":"2023-02-20T08:16:21Z","date_updated":"2023-02-24T09:28:04Z","year":"2015","publisher":"Elsevier","publication_status":"published","extern":"1","doi":"10.1016/j.advwatres.2015.01.013","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0309-1708"]},"month":"04","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12630","intvolume":" 78","title":"Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model","status":"public","issue":"4","abstract":[{"lang":"eng","text":"The hydrology of high-elevation watersheds of the Hindu Kush-Himalaya region (HKH) is poorly known. The correct representation of internal states and process dynamics in glacio-hydrological models can often not be verified due to missing in situ measurements. We use a new set of detailed ground data from the upper Langtang valley in Nepal to systematically guide a state-of-the art glacio-hydrological model through a parameter assigning process with the aim to understand the hydrology of the catchment and contribution of snow and ice processes to runoff. 14 parameters are directly calculated on the basis of local data, and 13 parameters are calibrated against 5 different datasets of in situ or remote sensing data. Spatial fields of debris thickness are reconstructed through a novel approach that employs data from an Unmanned Aerial Vehicle (UAV), energy balance modeling and statistical techniques. The model is validated against measured catchment runoff (Nash–Sutcliffe efficiency 0.87) and modeled snow cover is compared to Landsat snow cover. The advanced representation of processes allowed assessing the role played by avalanching for runoff for the first time for a Himalayan catchment (5% of annual water inputs to the hydrological system are due to snow redistribution) and to quantify the hydrological significance of sub-debris ice melt (9% of annual water inputs). Snowmelt is the most important contributor to total runoff during the hydrological year 2012/2013 (representing 40% of all sources), followed by rainfall (34%) and ice melt (26%). A sensitivity analysis is used to assess the efficiency of the monitoring network and identify the timing and location of field measurements that constrain model uncertainty. The methodology to set up a glacio-hydrological model in high-elevation regions presented in this study can be regarded as a benchmark for modelers in the HKH seeking to evaluate their calibration approach, their experimental setup and thus to reduce the predictive model uncertainty.\r\n\r\n"}],"type":"journal_article","date_published":"2015-04-01T00:00:00Z","citation":{"apa":"Ragettli, S., Pellicciotti, F., Immerzeel, W. W., Miles, E. S., Petersen, L., Heynen, M., … Shrestha, A. (2015). Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. Elsevier. https://doi.org/10.1016/j.advwatres.2015.01.013","ieee":"S. Ragettli et al., “Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model,” Advances in Water Resources, vol. 78, no. 4. Elsevier, pp. 94–111, 2015.","ista":"Ragettli S, Pellicciotti F, Immerzeel WW, Miles ES, Petersen L, Heynen M, Shea JM, Stumm D, Joshi S, Shrestha A. 2015. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. 78(4), 94–111.","ama":"Ragettli S, Pellicciotti F, Immerzeel WW, et al. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. 2015;78(4):94-111. doi:10.1016/j.advwatres.2015.01.013","chicago":"Ragettli, S., Francesca Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, and A. Shrestha. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources. Elsevier, 2015. https://doi.org/10.1016/j.advwatres.2015.01.013.","short":"S. Ragettli, F. Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, A. Shrestha, Advances in Water Resources 78 (2015) 94–111.","mla":"Ragettli, S., et al. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources, vol. 78, no. 4, Elsevier, 2015, pp. 94–111, doi:10.1016/j.advwatres.2015.01.013."},"publication":"Advances in Water Resources","page":"94-111","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Water Science and Technology"]},{"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.3189/2015JoG13J237","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.3189/2015jog13j237","month":"03","publication_identifier":{"issn":["0022-1430"],"eissn":["1727-5652"]},"publication_status":"published","publisher":"International Glaciological Society","year":"2015","date_updated":"2023-02-24T09:35:21Z","date_created":"2023-02-20T08:16:11Z","volume":61,"author":[{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca","full_name":"Pellicciotti, Francesca"},{"first_name":"Christa","last_name":"Stephan","full_name":"Stephan, Christa"},{"full_name":"Miles, Evan","first_name":"Evan","last_name":"Miles"},{"last_name":"Herreid","first_name":"Sam","full_name":"Herreid, Sam"},{"last_name":"Immerzeel","first_name":"Walter W.","full_name":"Immerzeel, Walter W."},{"last_name":"Bolch","first_name":"Tobias","full_name":"Bolch, Tobias"}],"extern":"1","article_type":"original","page":"373-386","publication":"Journal of Glaciology","citation":{"ama":"Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. 2015;61(226):373-386. doi:10.3189/2015jog13j237","apa":"Pellicciotti, F., Stephan, C., Miles, E., Herreid, S., Immerzeel, W. W., & Bolch, T. (2015). Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog13j237","ieee":"F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W. W. Immerzeel, and T. Bolch, “Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999,” Journal of Glaciology, vol. 61, no. 226. International Glaciological Society, pp. 373–386, 2015.","ista":"Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. 2015. Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. 61(226), 373–386.","short":"F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W.W. Immerzeel, T. Bolch, Journal of Glaciology 61 (2015) 373–386.","mla":"Pellicciotti, Francesca, et al. “Mass-Balance Changes of the Debris-Covered Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology, vol. 61, no. 226, International Glaciological Society, 2015, pp. 373–86, doi:10.3189/2015jog13j237.","chicago":"Pellicciotti, Francesca, Christa Stephan, Evan Miles, Sam Herreid, Walter W. Immerzeel, and Tobias Bolch. “Mass-Balance Changes of the Debris-Covered Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog13j237."},"date_published":"2015-03-01T00:00:00Z","keyword":["Earth-Surface Processes"],"scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999","intvolume":" 61","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12628","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Thick debris cover on glaciers can significantly reduce ice melt. However, several studies have suggested that debris-covered glaciers in the Himalaya might have lost mass at a rate similar to debris-free glaciers. We reconstruct elevation and mass changes for the debris-covered glaciers of the upper Langtang valley, Nepalese Himalaya, using a digital elevation model (DEM) from 1974 stereo Hexagon satellite data and the 2000 SRTM (Shuttle Radar Topography Mission) DEM. Uncertainties are high in the accumulation areas, due to data gaps in the SRTM and difficulties with delineation of the glacier borders. Even with these uncertainties, we obtain thinning rates comparable to those of several other studies in the Himalaya. In particular, we obtain a total mass balance for the investigated debris-covered glaciers of the basin of –0.32 ± 0.18 m w.e. a−1. However, there are major spatial differences both between glaciers and within any single glacier, exhibiting a very distinct nonlinear mass-balance profile with elevation. Through analysis of surface velocities derived from Landsat ETM+ imagery, we show that thinning occurs in areas of low velocity and low slope. These areas are prone to a general, dynamic decay of surface features and to the development of supraglacial lakes and ice cliffs, which may be responsible for a considerable increase in overall glacier ablation."}],"issue":"226"},{"oa_version":"Published Version","_id":"12631","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming","status":"public","intvolume":" 120","abstract":[{"lang":"eng","text":"Air temperature is one of the most relevant input variables for snow and ice melt calculations. However, local meteorological conditions, complex topography, and logistical concerns in glacierized regions make the measuring and modeling of air temperature a difficult task. In this study, we investigate the spatial distribution of 2 m air temperature over mountain glaciers and propose a modification to an existing model to improve its representation. Spatially distributed meteorological data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte (Chile) Glaciers are used to examine approximate flow line temperatures during their respective ablation seasons. During warm conditions (off-glacier temperatures well above 0°C), observed air temperatures in the upper reaches of Place Glacier and Haut Glacier d'Arolla decrease down glacier along the approximate flow line. At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed over the glacier tongue. While the temperature behavior over the upper part can be explained by the cooling effect of the glacier surface, the temperature increase over the glacier tongue may be caused by several processes induced by the surrounding warm atmosphere. In order to capture the latter effect, we add an additional term to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier temperatures, the modified GB model reduces root-mean-square error up to 32% and provides a new approach for distributing air temperature over mountain glaciers as a function of off-glacier temperatures and approximate glacier flow lines."}],"issue":"8","type":"journal_article","date_published":"2015-04-18T00:00:00Z","publication":"Journal of Geophysical Research: Atmospheres","citation":{"ama":"Ayala A, Pellicciotti F, Shea JM. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 2015;120(8):3139-3157. doi:10.1002/2015jd023137","ista":"Ayala A, Pellicciotti F, Shea JM. 2015. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 120(8), 3139–3157.","apa":"Ayala, A., Pellicciotti, F., & Shea, J. M. (2015). Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. American Geophysical Union. https://doi.org/10.1002/2015jd023137","ieee":"A. Ayala, F. Pellicciotti, and J. M. Shea, “Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming,” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8. American Geophysical Union, pp. 3139–3157, 2015.","mla":"Ayala, A., et al. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8, American Geophysical Union, 2015, pp. 3139–57, doi:10.1002/2015jd023137.","short":"A. Ayala, F. Pellicciotti, J.M. Shea, Journal of Geophysical Research: Atmospheres 120 (2015) 3139–3157.","chicago":"Ayala, A., Francesca Pellicciotti, and J. M. Shea. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres. American Geophysical Union, 2015. https://doi.org/10.1002/2015jd023137."},"article_type":"original","page":"3139-3157","day":"18","article_processing_charge":"No","scopus_import":"1","keyword":["Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Geophysics"],"author":[{"first_name":"A.","last_name":"Ayala","full_name":"Ayala, A."},{"last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"},{"first_name":"J. M.","last_name":"Shea","full_name":"Shea, J. M."}],"date_created":"2023-02-20T08:16:28Z","date_updated":"2023-02-24T09:16:26Z","volume":120,"year":"2015","publication_status":"published","publisher":"American Geophysical Union","extern":"1","doi":"10.1002/2015jd023137","language":[{"iso":"eng"}],"quality_controlled":"1","month":"04","publication_identifier":{"issn":["2169-897X"],"eissn":["2169-8996"]}},{"publisher":"Taylor & Francis","publication_status":"published","year":"2015","volume":31,"date_created":"2023-02-20T08:16:17Z","date_updated":"2023-02-24T09:30:42Z","author":[{"full_name":"Shea, J.M.","last_name":"Shea","first_name":"J.M."},{"first_name":"P.","last_name":"Wagnon","full_name":"Wagnon, P."},{"last_name":"Immerzeel","first_name":"W.W.","full_name":"Immerzeel, W.W."},{"full_name":"Biron, R.","last_name":"Biron","first_name":"R."},{"full_name":"Brun, F.","first_name":"F.","last_name":"Brun"},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca"}],"extern":"1","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/07900627.2015.1020417"}],"language":[{"iso":"eng"}],"doi":"10.1080/07900627.2015.1020417","publication_identifier":{"eissn":["1360-0648"],"issn":["0790-0627"]},"month":"04","intvolume":" 31","status":"public","title":"A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12629","oa_version":"Published Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Meteorological studies in high-mountain environments form the basis of our understanding of catchment hydrology and glacier accumulation and melt processes, yet high-altitude (>4000 m above sea level, asl) observatories are rare. This research presents meteorological data recorded between December 2012 and November 2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl. Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation are compared between sites. Solar radiation strongly affects diurnal temperature and vapour pressure cycles, but local topography and valley-scale circulations alter wind speed and precipitation cycles. The observed diurnal variability in vertical temperature gradients in all seasons highlights the importance of in situ measurements for melt modelling. The monsoon signal (progressive onset and sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon Phailin in mid-October 2013 provides an interesting case study on the possible effects of such storms on glaciers in the region."}],"page":"174-200","article_type":"original","citation":{"ista":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. 2015. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 31(2), 174–200.","apa":"Shea, J. M., Wagnon, P., Immerzeel, W. W., Biron, R., Brun, F., & Pellicciotti, F. (2015). A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. Taylor & Francis. https://doi.org/10.1080/07900627.2015.1020417","ieee":"J. M. Shea, P. Wagnon, W. W. Immerzeel, R. Biron, F. Brun, and F. Pellicciotti, “A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya,” International Journal of Water Resources Development, vol. 31, no. 2. Taylor & Francis, pp. 174–200, 2015.","ama":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 2015;31(2):174-200. doi:10.1080/07900627.2015.1020417","chicago":"Shea, J.M., P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, and Francesca Pellicciotti. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development. Taylor & Francis, 2015. https://doi.org/10.1080/07900627.2015.1020417.","mla":"Shea, J. M., et al. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development, vol. 31, no. 2, Taylor & Francis, 2015, pp. 174–200, doi:10.1080/07900627.2015.1020417.","short":"J.M. Shea, P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, F. Pellicciotti, International Journal of Water Resources Development 31 (2015) 174–200."},"publication":"International Journal of Water Resources Development","date_published":"2015-04-18T00:00:00Z","keyword":["Water Science and Technology","Development"],"scopus_import":"1","article_processing_charge":"No","day":"18"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Ice cliffs have been identified as a reason for higher ablation rates on debris-covered glaciers than are implied by the insulation effects of the debris. This study aims to improve our understanding of cliff backwasting, and the role of radiative fluxes in particular. An energy-balance model is forced with new data gathered in May and October 2013 on Lirung Glacier, Nepalese Himalaya. Observations show substantial variability in melt between cliffs, between locations on any cliff and between seasons. Using a high-resolution digital elevation model we calculate longwave fluxes incident to the cliff from surrounding terrain and include the effect of local shading on shortwave radiation. This is an advance over previous studies, that made simplified assumptions on cliff geometry and radiative fluxes. Measured melt rates varied between 3.25 and 8.6 cm d−1 in May and 0.18 and 1.34 cm d−1 in October. Model results reproduce the strong variability in space and time, suggesting considerable differences in radiative fluxes over one cliff. In October the model fails to reproduce stake readings, probably due to the lack of a refreezing component. Disregarding local topography can lead to overestimation of melt at the point scale by up to ∼9%."}],"issue":"229","status":"public","title":"Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya","intvolume":" 61","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12626","oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"889-907","publication":"Journal of Glaciology","citation":{"chicago":"Steiner, Jakob F., Francesca Pellicciotti, Pascal Buri, Evan S. Miles, Walter W. Immerzeel, and Tim D. Reid. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j194.","mla":"Steiner, Jakob F., et al. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology, vol. 61, no. 229, International Glaciological Society, 2015, pp. 889–907, doi:10.3189/2015jog14j194.","short":"J.F. Steiner, F. Pellicciotti, P. Buri, E.S. Miles, W.W. Immerzeel, T.D. Reid, Journal of Glaciology 61 (2015) 889–907.","ista":"Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. 2015. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 61(229), 889–907.","apa":"Steiner, J. F., Pellicciotti, F., Buri, P., Miles, E. S., Immerzeel, W. W., & Reid, T. D. (2015). Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j194","ieee":"J. F. Steiner, F. Pellicciotti, P. Buri, E. S. Miles, W. W. Immerzeel, and T. D. Reid, “Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya,” Journal of Glaciology, vol. 61, no. 229. International Glaciological Society, pp. 889–907, 2015.","ama":"Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 2015;61(229):889-907. doi:10.3189/2015jog14j194"},"date_published":"2015-07-01T00:00:00Z","extern":"1","publication_status":"published","publisher":"International Glaciological Society","year":"2015","date_updated":"2023-02-24T09:43:14Z","date_created":"2023-02-20T08:16:01Z","volume":61,"author":[{"first_name":"Jakob F.","last_name":"Steiner","full_name":"Steiner, Jakob F."},{"last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"},{"first_name":"Pascal","last_name":"Buri","full_name":"Buri, Pascal"},{"full_name":"Miles, Evan S.","first_name":"Evan S.","last_name":"Miles"},{"full_name":"Immerzeel, Walter W.","first_name":"Walter W.","last_name":"Immerzeel"},{"full_name":"Reid, Tim D.","last_name":"Reid","first_name":"Tim D."}],"month":"07","publication_identifier":{"issn":["0022-1430"],"eissn":["1727-5652"]},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.3189/2015JoG14J194"}],"language":[{"iso":"eng"}],"doi":"10.3189/2015jog14j194"},{"year":"2015","publication_status":"published","publisher":"International Glaciological Society","author":[{"full_name":"Herreid, Sam","last_name":"Herreid","first_name":"Sam"},{"last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"},{"last_name":"Ayala","first_name":"Alvaro","full_name":"Ayala, Alvaro"},{"first_name":"Anna","last_name":"Chesnokova","full_name":"Chesnokova, Anna"},{"full_name":"Kienholz, Christian","first_name":"Christian","last_name":"Kienholz"},{"full_name":"Shea, Joseph","first_name":"Joseph","last_name":"Shea"},{"first_name":"Arun","last_name":"Shrestha","full_name":"Shrestha, Arun"}],"date_created":"2023-02-20T08:16:06Z","date_updated":"2023-02-24T09:40:30Z","volume":61,"extern":"1","main_file_link":[{"url":"https://doi.org/10.3189/2015JoG14J227","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.3189/2015jog14j227","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12627","title":"Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014","status":"public","intvolume":" 61","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Spatial evolution of supraglacial debris cover on mountain glaciers is a largely unmonitored and poorly understood phenomenon that directly affects glacier melt. Supraglacial debris cover for 93 glaciers in the Karakoram, northern Pakistan, was mapped from Landsat imagery acquired in 1977, 1998, 2009 and 2014. Surge-type glaciers occupy 41% of the study area and were considered separately. The time series of debris-covered surface area change shows a mean value of zero or near-zero change for both surging and non-surging glaciers. An increase in debris-covered area is often associated with negative regional mass balances. We extend this logic to suggest that the stable regional mass balances in the Karakoram explain the zero or near-zero change in debris-covered area. This coupling of trends combined with our 37 year time series of data suggests the Karakoram anomaly extends further back in time than previously known."}],"issue":"227","publication":"Journal of Glaciology","citation":{"ista":"Herreid S, Pellicciotti F, Ayala A, Chesnokova A, Kienholz C, Shea J, Shrestha A. 2015. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 61(227), 524–536.","ieee":"S. Herreid et al., “Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014,” Journal of Glaciology, vol. 61, no. 227. International Glaciological Society, pp. 524–536, 2015.","apa":"Herreid, S., Pellicciotti, F., Ayala, A., Chesnokova, A., Kienholz, C., Shea, J., & Shrestha, A. (2015). Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j227","ama":"Herreid S, Pellicciotti F, Ayala A, et al. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 2015;61(227):524-536. doi:10.3189/2015jog14j227","chicago":"Herreid, Sam, Francesca Pellicciotti, Alvaro Ayala, Anna Chesnokova, Christian Kienholz, Joseph Shea, and Arun Shrestha. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j227.","mla":"Herreid, Sam, et al. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology, vol. 61, no. 227, International Glaciological Society, 2015, pp. 524–36, doi:10.3189/2015jog14j227.","short":"S. Herreid, F. Pellicciotti, A. Ayala, A. Chesnokova, C. Kienholz, J. Shea, A. Shrestha, Journal of Glaciology 61 (2015) 524–536."},"article_type":"original","page":"524-536","date_published":"2015-05-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"publication":"Biochemistry","citation":{"ama":"Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 2015;54(27):4163-4166. doi:10.1021/acs.biochem.5b00560","ista":"Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H, Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 54(27), 4163–4166.","ieee":"C. Veldkamp et al., “Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites,” Biochemistry, vol. 54, no. 27. American Chemical Society, pp. 4163–4166, 2015.","apa":"Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D., Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. American Chemical Society. https://doi.org/10.1021/acs.biochem.5b00560","mla":"Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry, vol. 54, no. 27, American Chemical Society, 2015, pp. 4163–66, doi:10.1021/acs.biochem.5b00560.","short":"C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F. Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey, Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson, A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K. Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166.","chicago":"Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer, David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry. American Chemical Society, 2015. https://doi.org/10.1021/acs.biochem.5b00560."},"page":"4163 - 4166","date_published":"2015-06-26T00:00:00Z","scopus_import":"1","day":"26","article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1618","status":"public","title":"Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites","intvolume":" 54","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed.","lang":"eng"}],"issue":"27","external_id":{"pmid":["26115234"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/"}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"}],"doi":"10.1021/acs.biochem.5b00560","language":[{"iso":"eng"}],"month":"06","year":"2015","pmid":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MiSi"}],"author":[{"full_name":"Veldkamp, Christopher","last_name":"Veldkamp","first_name":"Christopher"},{"full_name":"Kiermaier, Eva","last_name":"Kiermaier","first_name":"Eva","orcid":"0000-0001-6165-5738","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gabel Eissens, Skylar","first_name":"Skylar","last_name":"Gabel Eissens"},{"full_name":"Gillitzer, Miranda","last_name":"Gillitzer","first_name":"Miranda"},{"full_name":"Lippner, David","first_name":"David","last_name":"Lippner"},{"full_name":"Disilvio, Frank","first_name":"Frank","last_name":"Disilvio"},{"full_name":"Mueller, Casey","first_name":"Casey","last_name":"Mueller"},{"full_name":"Wantuch, Paeton","last_name":"Wantuch","first_name":"Paeton"},{"last_name":"Chaffee","first_name":"Gary","full_name":"Chaffee, Gary"},{"full_name":"Famiglietti, Michael","first_name":"Michael","last_name":"Famiglietti"},{"full_name":"Zgoba, Danielle","last_name":"Zgoba","first_name":"Danielle"},{"full_name":"Bailey, Asha","last_name":"Bailey","first_name":"Asha"},{"last_name":"Bah","first_name":"Yaya","full_name":"Bah, Yaya"},{"full_name":"Engebretson, Samantha","last_name":"Engebretson","first_name":"Samantha"},{"full_name":"Graupner, David","first_name":"David","last_name":"Graupner"},{"full_name":"Lackner, Emily","first_name":"Emily","last_name":"Lackner"},{"full_name":"Larosa, Vincent","first_name":"Vincent","last_name":"Larosa"},{"last_name":"Medeiros","first_name":"Tysha","full_name":"Medeiros, Tysha"},{"first_name":"Michael","last_name":"Olson","full_name":"Olson, Michael"},{"full_name":"Phillips, Andrew","last_name":"Phillips","first_name":"Andrew"},{"last_name":"Pyles","first_name":"Harley","full_name":"Pyles, Harley"},{"full_name":"Richard, Amanda","first_name":"Amanda","last_name":"Richard"},{"last_name":"Schoeller","first_name":"Scott","full_name":"Schoeller, Scott"},{"last_name":"Touzeau","first_name":"Boris","full_name":"Touzeau, Boris"},{"full_name":"Williams, Larry","last_name":"Williams","first_name":"Larry"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"full_name":"Peterson, Francis","last_name":"Peterson","first_name":"Francis"}],"date_updated":"2023-03-30T11:32:57Z","date_created":"2018-12-11T11:53:03Z","volume":54,"ec_funded":1,"publist_id":"5548"},{"type":"conference","file":[{"date_updated":"2023-05-02T07:02:59Z","date_created":"2023-05-02T07:02:59Z","checksum":"880eabe59c9df12f06a882aa1bc4e600","success":1,"relation":"main_file","file_id":"12882","file_size":1674241,"content_type":"application/pdf","creator":"dernst","file_name":"2015_ECAL_Martius.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12881","status":"public","ddc":["000"],"title":"Quantifying self-organizing behavior of autonomous robots","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2015-07-01T00:00:00Z","publication":"Proceedings of the 13th European Conference on Artificial Life","citation":{"ista":"Martius GS, Olbrich E. 2015. Quantifying self-organizing behavior of autonomous robots. Proceedings of the 13th European Conference on Artificial Life. ECAL: European Conference on Artificial Life, 78.","ieee":"G. S. Martius and E. Olbrich, “Quantifying self-organizing behavior of autonomous robots,” in Proceedings of the 13th European Conference on Artificial Life, York, United Kingdom, 2015, p. 78.","apa":"Martius, G. S., & Olbrich, E. (2015). Quantifying self-organizing behavior of autonomous robots. In Proceedings of the 13th European Conference on Artificial Life (p. 78). York, United Kingdom: MIT Press. https://doi.org/10.7551/978-0-262-33027-5-ch018","ama":"Martius GS, Olbrich E. Quantifying self-organizing behavior of autonomous robots. In: Proceedings of the 13th European Conference on Artificial Life. MIT Press; 2015:78. doi:10.7551/978-0-262-33027-5-ch018","chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” In Proceedings of the 13th European Conference on Artificial Life, 78. MIT Press, 2015. https://doi.org/10.7551/978-0-262-33027-5-ch018.","mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78, doi:10.7551/978-0-262-33027-5-ch018.","short":"G.S. Martius, E. Olbrich, in:, Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78."},"page":"78","file_date_updated":"2023-05-02T07:02:59Z","ec_funded":1,"author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"},{"full_name":"Olbrich, Eckehard","last_name":"Olbrich","first_name":"Eckehard"}],"date_updated":"2023-05-02T07:06:21Z","date_created":"2023-04-30T22:01:07Z","acknowledgement":"This work was supported by the DFG (SPP 1527) and the EU (FP7, REA grant no 291734).","year":"2015","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"MIT Press","month":"07","publication_identifier":{"isbn":["9780262330275"]},"conference":{"end_date":"2015-07-24","location":"York, United Kingdom","start_date":"2015-07-20","name":"ECAL: European Conference on Artificial Life"},"doi":"10.7551/978-0-262-33027-5-ch018","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"month":"08","publication_identifier":{"issn":["0032-0781","1471-9053"]},"language":[{"iso":"eng"}],"doi":"10.1093/pcp/pcv087","quality_controlled":"1","external_id":{"pmid":["26063389"]},"extern":"1","date_created":"2023-01-16T09:20:22Z","date_updated":"2023-05-08T11:03:23Z","volume":56,"author":[{"full_name":"Johnson, Kaeli C.M.","last_name":"Johnson","first_name":"Kaeli C.M."},{"last_name":"Xia","first_name":"Shitou","full_name":"Xia, Shitou"},{"orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi"},{"full_name":"Li, Xin","last_name":"Li","first_name":"Xin"}],"publication_status":"published","department":[{"_id":"XiFe"}],"publisher":"Oxford University Press","acknowledgement":"This work was supported by the National Sciences and Engineering Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles Copeland for critical reading of the manuscript.","year":"2015","pmid":1,"article_processing_charge":"No","keyword":["Cell Biology","Plant Science","Physiology","General Medicine"],"scopus_import":"1","date_published":"2015-08-01T00:00:00Z","article_type":"original","page":"1616-1623","publication":"Plant and Cell Physiology","citation":{"chicago":"Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology. Oxford University Press, 2015. https://doi.org/10.1093/pcp/pcv087.","mla":"Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology, vol. 56, no. 8, Oxford University Press, 2015, pp. 1616–23, doi:10.1093/pcp/pcv087.","short":"K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015) 1616–1623.","ista":"Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623.","ieee":"K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity,” Plant and Cell Physiology, vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.","apa":"Johnson, K. C. M., Xia, S., Feng, X., & Li, X. (2015). The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcv087","ama":"Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 2015;56(8):1616-1623. doi:10.1093/pcp/pcv087"},"abstract":[{"text":"SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity.","lang":"eng"}],"issue":"8","type":"journal_article","oa_version":"None","title":"The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity","status":"public","intvolume":" 56","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12196"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13392","status":"public","title":"Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks","intvolume":" 11","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","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."}],"publication":"Nature Nanotechnology","citation":{"ama":"Zhao H, Sen S, Udayabhaskararao T, et al. Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. 2015;11:82-88. doi:10.1038/nnano.2015.256","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.","ieee":"H. Zhao et al., “Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks,” Nature Nanotechnology, vol. 11. Springer Nature, pp. 82–88, 2015.","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. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/nnano.2015.256","mla":"Zhao, Hui, et al. “Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.” Nature Nanotechnology, vol. 11, Springer Nature, 2015, pp. 82–88, doi:10.1038/nnano.2015.256.","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.” Nature Nanotechnology. Springer Nature, 2015. https://doi.org/10.1038/nnano.2015.256."},"article_type":"original","page":"82-88","date_published":"2015-11-23T00:00:00Z","scopus_import":"1","keyword":["Electrical and Electronic Engineering","Condensed Matter Physics","General Materials Science","Biomedical Engineering","Atomic and Molecular Physics","and Optics","Bioengineering"],"day":"23","article_processing_charge":"No","year":"2015","pmid":1,"publication_status":"published","publisher":"Springer Nature","author":[{"first_name":"Hui","last_name":"Zhao","full_name":"Zhao, Hui"},{"full_name":"Sen, Soumyo","last_name":"Sen","first_name":"Soumyo"},{"first_name":"T.","last_name":"Udayabhaskararao","full_name":"Udayabhaskararao, T."},{"last_name":"Sawczyk","first_name":"Michał","full_name":"Sawczyk, Michał"},{"last_name":"Kučanda","first_name":"Kristina","full_name":"Kučanda, Kristina"},{"first_name":"Debasish","last_name":"Manna","full_name":"Manna, Debasish"},{"last_name":"Kundu","first_name":"Pintu K.","full_name":"Kundu, Pintu K."},{"first_name":"Ji-Woong","last_name":"Lee","full_name":"Lee, Ji-Woong"},{"full_name":"Král, Petr","first_name":"Petr","last_name":"Král"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal"}],"date_updated":"2023-08-07T12:55:46Z","date_created":"2023-08-01T09:44:04Z","volume":11,"extern":"1","external_id":{"pmid":["26595335"]},"quality_controlled":"1","doi":"10.1038/nnano.2015.256","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]}},{"doi":"10.1038/nchem.2303","language":[{"iso":"eng"}],"external_id":{"pmid":["26201741"]},"quality_controlled":"1","month":"07","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"author":[{"last_name":"Kundu","first_name":"Pintu K.","full_name":"Kundu, Pintu K."},{"full_name":"Samanta, Dipak","last_name":"Samanta","first_name":"Dipak"},{"last_name":"Leizrowice","first_name":"Ron","full_name":"Leizrowice, Ron"},{"last_name":"Margulis","first_name":"Baruch","full_name":"Margulis, Baruch"},{"full_name":"Zhao, Hui","last_name":"Zhao","first_name":"Hui"},{"first_name":"Martin","last_name":"Börner","full_name":"Börner, Martin"},{"first_name":"T.","last_name":"Udayabhaskararao","full_name":"Udayabhaskararao, T."},{"first_name":"Debasish","last_name":"Manna","full_name":"Manna, Debasish"},{"last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}],"date_created":"2023-08-01T09:44:33Z","date_updated":"2023-08-07T13:00:15Z","volume":7,"year":"2015","pmid":1,"publication_status":"published","publisher":"Springer Nature","extern":"1","date_published":"2015-07-20T00:00:00Z","publication":"Nature Chemistry","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. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.2303","ieee":"P. K. Kundu et al., “Light-controlled self-assembly of non-photoresponsive nanoparticles,” Nature Chemistry, vol. 7. Springer Nature, pp. 646–652, 2015.","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.","ama":"Kundu PK, Samanta D, Leizrowice R, et al. Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. 2015;7:646-652. doi:10.1038/nchem.2303","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.” Nature Chemistry. Springer Nature, 2015. https://doi.org/10.1038/nchem.2303.","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.","mla":"Kundu, Pintu K., et al. “Light-Controlled Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry, vol. 7, Springer Nature, 2015, pp. 646–52, doi:10.1038/nchem.2303."},"article_type":"original","page":"646-652","day":"20","article_processing_charge":"No","scopus_import":"1","keyword":["General Chemical Engineering","General Chemistry"],"oa_version":"None","_id":"13394","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Light-controlled self-assembly of non-photoresponsive nanoparticles","status":"public","intvolume":" 7","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."}],"type":"journal_article"},{"scopus_import":"1","keyword":["General Chemistry","Catalysis"],"article_processing_charge":"No","day":"01","citation":{"ama":"Manna D, Udayabhaskararao T, Zhao H, Klajn R. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. 2015;54(42):12394-12397. doi:10.1002/anie.201502419","apa":"Manna, D., Udayabhaskararao, T., Zhao, H., & Klajn, R. (2015). Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201502419","ieee":"D. Manna, T. Udayabhaskararao, H. Zhao, and R. Klajn, “Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes,” Angewandte Chemie International Edition, vol. 54, no. 42. Wiley, pp. 12394–12397, 2015.","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.","short":"D. Manna, T. Udayabhaskararao, H. Zhao, R. Klajn, Angewandte Chemie International Edition 54 (2015) 12394–12397.","mla":"Manna, Debasish, et al. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” Angewandte Chemie International Edition, vol. 54, no. 42, Wiley, 2015, pp. 12394–97, doi:10.1002/anie.201502419.","chicago":"Manna, Debasish, Thumu Udayabhaskararao, Hui Zhao, and Rafal Klajn. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” Angewandte Chemie International Edition. Wiley, 2015. https://doi.org/10.1002/anie.201502419."},"publication":"Angewandte Chemie International Edition","page":"12394-12397","article_type":"original","date_published":"2015-10-01T00:00:00Z","type":"journal_article","issue":"42","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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13393","intvolume":" 54","title":"Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes","status":"public","oa_version":"None","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"month":"10","external_id":{"pmid":["25959725"]},"quality_controlled":"1","doi":"10.1002/anie.201502419","language":[{"iso":"eng"}],"extern":"1","pmid":1,"year":"2015","publisher":"Wiley","publication_status":"published","author":[{"last_name":"Manna","first_name":"Debasish","full_name":"Manna, Debasish"},{"full_name":"Udayabhaskararao, Thumu","last_name":"Udayabhaskararao","first_name":"Thumu"},{"last_name":"Zhao","first_name":"Hui","full_name":"Zhao, Hui"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"volume":54,"date_created":"2023-08-01T09:44:19Z","date_updated":"2023-08-07T12:58:29Z"},{"month":"11","publication_identifier":{"issn":["1359-7345"],"eissn":["1364-548X"]},"language":[{"iso":"eng"}],"doi":"10.1039/c4cc08541h","quality_controlled":"1","external_id":{"pmid":["25417754"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/C4CC08541H"}],"extern":"1","date_created":"2023-08-01T09:44:48Z","date_updated":"2023-08-07T13:01:53Z","volume":51,"author":[{"last_name":"Lee","first_name":"Ji-Woong","full_name":"Lee, Ji-Woong"},{"last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}],"publication_status":"published","publisher":"Royal Society of Chemistry","year":"2015","pmid":1,"day":"18","article_processing_charge":"No","keyword":["Materials Chemistry","Metals and Alloys","Surfaces","Coatings and Films","General Chemistry","Ceramics and Composites","Electronic","Optical and Magnetic Materials","Catalysis"],"scopus_import":"1","date_published":"2015-11-18T00:00:00Z","article_type":"original","page":"2036-2039","publication":"Chemical Communications","citation":{"ieee":"J.-W. Lee and R. Klajn, “Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2,” Chemical Communications, vol. 51, no. 11. Royal Society of Chemistry, pp. 2036–2039, 2015.","apa":"Lee, J.-W., & Klajn, R. (2015). Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/c4cc08541h","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.","ama":"Lee J-W, Klajn R. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. 2015;51(11):2036-2039. doi:10.1039/c4cc08541h","chicago":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” Chemical Communications. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4cc08541h.","short":"J.-W. Lee, R. Klajn, Chemical Communications 51 (2015) 2036–2039.","mla":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” Chemical Communications, vol. 51, no. 11, Royal Society of Chemistry, 2015, pp. 2036–39, doi:10.1039/c4cc08541h."},"abstract":[{"lang":"eng","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."}],"issue":"11","type":"journal_article","oa_version":"Published Version","status":"public","title":"Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2","intvolume":" 51","_id":"13395","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"extern":"1","year":"2015","pmid":1,"publication_status":"published","publisher":"American Chemical Society","author":[{"last_name":"Moldt","first_name":"Thomas","full_name":"Moldt, Thomas"},{"first_name":"Daniel","last_name":"Brete","full_name":"Brete, Daniel"},{"full_name":"Przyrembel, Daniel","first_name":"Daniel","last_name":"Przyrembel"},{"full_name":"Das, Sanjib","first_name":"Sanjib","last_name":"Das"},{"first_name":"Joel R.","last_name":"Goldman","full_name":"Goldman, Joel R."},{"first_name":"Pintu K.","last_name":"Kundu","full_name":"Kundu, Pintu K."},{"last_name":"Gahl","first_name":"Cornelius","full_name":"Gahl, Cornelius"},{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"full_name":"Weinelt, Martin","last_name":"Weinelt","first_name":"Martin"}],"date_created":"2023-08-01T09:45:02Z","date_updated":"2023-08-07T13:05:04Z","volume":31,"month":"01","publication_identifier":{"eissn":["1520-5827"],"issn":["0743-7463"]},"external_id":{"pmid":["25544061"]},"quality_controlled":"1","doi":"10.1021/la504291n","language":[{"iso":"eng"}],"type":"journal_article","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"}],"issue":"3","_id":"13396","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature","intvolume":" 31","oa_version":"None","scopus_import":"1","keyword":["Electrochemistry","Spectroscopy","Surfaces and Interfaces","Condensed Matter Physics","General Materials Science"],"day":"27","article_processing_charge":"No","publication":"Langmuir","citation":{"ama":"Moldt T, Brete D, Przyrembel D, et al. Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. 2015;31(3):1048-1057. doi:10.1021/la504291n","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.","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. Langmuir. American Chemical Society. https://doi.org/10.1021/la504291n","ieee":"T. Moldt et al., “Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature,” Langmuir, vol. 31, no. 3. American Chemical Society, pp. 1048–1057, 2015.","mla":"Moldt, Thomas, et al. “Tailoring the Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface Curvature.” Langmuir, vol. 31, no. 3, American Chemical Society, 2015, pp. 1048–57, doi:10.1021/la504291n.","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.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/la504291n."},"article_type":"original","page":"1048-1057","date_published":"2015-01-27T00:00:00Z"},{"status":"public","title":"Magnetic field-induced self-assembly of iron oxide nanocubes","intvolume":" 181","_id":"13397","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","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."}],"article_type":"original","page":"403-421","publication":"Faraday Discussions","citation":{"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.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4fd00265b.","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.","mla":"Singh, Gurvinder, et al. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 403–21, doi:10.1039/c4fd00265b.","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. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c4fd00265b","ieee":"G. Singh et al., “Magnetic field-induced self-assembly of iron oxide nanocubes,” Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 403–421, 2015.","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.","ama":"Singh G, Chan H, Udayabhaskararao T, et al. Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. 2015;181:403-421. doi:10.1039/c4fd00265b"},"date_published":"2015-01-02T00:00:00Z","keyword":["Physical and Theoretical Chemistry"],"scopus_import":"1","day":"02","article_processing_charge":"No","publication_status":"published","publisher":"Royal Society of Chemistry","year":"2015","pmid":1,"date_updated":"2023-08-07T13:06:23Z","date_created":"2023-08-01T09:45:17Z","volume":181,"author":[{"full_name":"Singh, Gurvinder","last_name":"Singh","first_name":"Gurvinder"},{"last_name":"Chan","first_name":"Henry","full_name":"Chan, Henry"},{"full_name":"Udayabhaskararao, T.","first_name":"T.","last_name":"Udayabhaskararao"},{"full_name":"Gelman, Elijah","last_name":"Gelman","first_name":"Elijah"},{"full_name":"Peddis, Davide","last_name":"Peddis","first_name":"Davide"},{"full_name":"Baskin, Artem","first_name":"Artem","last_name":"Baskin"},{"full_name":"Leitus, Gregory","last_name":"Leitus","first_name":"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","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/C4FD00265B"}],"external_id":{"pmid":["25920522"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1039/c4fd00265b","month":"01","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]}},{"publication_identifier":{"eissn":["1364-5498"],"issn":["1359-6640"]},"month":"07","external_id":{"pmid":["26149295"]},"quality_controlled":"1","doi":"10.1039/c5fd90041g","language":[{"iso":"eng"}],"extern":"1","pmid":1,"year":"2015","publisher":"Royal Society of Chemistry","publication_status":"published","author":[{"full_name":"Sun, Yugang","last_name":"Sun","first_name":"Yugang"},{"full_name":"Scarabelli, Leonardo","first_name":"Leonardo","last_name":"Scarabelli"},{"full_name":"Kotov, Nicholas","last_name":"Kotov","first_name":"Nicholas"},{"first_name":"Moritz","last_name":"Tebbe","full_name":"Tebbe, Moritz"},{"full_name":"Lin, Xiao-Min","first_name":"Xiao-Min","last_name":"Lin"},{"last_name":"Brullot","first_name":"Ward","full_name":"Brullot, Ward"},{"first_name":"Lucio","last_name":"Isa","full_name":"Isa, Lucio"},{"full_name":"Schurtenberger, Peter","last_name":"Schurtenberger","first_name":"Peter"},{"full_name":"Moehwald, Helmuth","last_name":"Moehwald","first_name":"Helmuth"},{"full_name":"Fedin, Igor","last_name":"Fedin","first_name":"Igor"},{"full_name":"Velev, Orlin","first_name":"Orlin","last_name":"Velev"},{"first_name":"Damien","last_name":"Faivre","full_name":"Faivre, Damien"},{"full_name":"Sorensen, Christopher","first_name":"Christopher","last_name":"Sorensen"},{"full_name":"Perzynski, Régine","first_name":"Régine","last_name":"Perzynski"},{"full_name":"Chanana, Munish","last_name":"Chanana","first_name":"Munish"},{"last_name":"Li","first_name":"Zhihai","full_name":"Li, Zhihai"},{"full_name":"Bresme, Fernando","first_name":"Fernando","last_name":"Bresme"},{"full_name":"Král, Petr","last_name":"Král","first_name":"Petr"},{"full_name":"Firlar, Emre","last_name":"Firlar","first_name":"Emre"},{"first_name":"David","last_name":"Schiffrin","full_name":"Schiffrin, David"},{"first_name":"Joao Batista","last_name":"Souza Junior","full_name":"Souza Junior, Joao Batista"},{"full_name":"Fery, Andreas","last_name":"Fery","first_name":"Andreas"},{"first_name":"Elena","last_name":"Shevchenko","full_name":"Shevchenko, Elena"},{"first_name":"Ozgur","last_name":"Tarhan","full_name":"Tarhan, Ozgur"},{"first_name":"Armand Paul","last_name":"Alivisatos","full_name":"Alivisatos, Armand Paul"},{"full_name":"Disch, Sabrina","first_name":"Sabrina","last_name":"Disch"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"},{"last_name":"Ghosh","first_name":"Suvojit","full_name":"Ghosh, Suvojit"}],"volume":181,"date_created":"2023-08-01T09:45:29Z","date_updated":"2023-08-08T07:16:20Z","scopus_import":"1","keyword":["Physical and Theoretical Chemistry"],"article_processing_charge":"No","day":"07","citation":{"ama":"Sun Y, Scarabelli L, Kotov N, et al. Field-assisted self-assembly process: General discussion. Faraday Discussions. 2015;181:463-479. doi:10.1039/c5fd90041g","apa":"Sun, Y., Scarabelli, L., Kotov, N., Tebbe, M., Lin, X.-M., Brullot, W., … Ghosh, S. (2015). Field-assisted self-assembly process: General discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c5fd90041g","ieee":"Y. Sun et al., “Field-assisted self-assembly process: General discussion,” Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 463–479, 2015.","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.","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.","mla":"Sun, Yugang, et al. “Field-Assisted Self-Assembly Process: General Discussion.” Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 463–79, doi:10.1039/c5fd90041g.","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.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c5fd90041g."},"publication":"Faraday Discussions","page":"463-479","article_type":"letter_note","date_published":"2015-07-07T00:00:00Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13398","intvolume":" 181","status":"public","title":"Field-assisted self-assembly process: General discussion","oa_version":"None"},{"external_id":{"arxiv":["1504.03933"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.03933"}],"quality_controlled":"1","doi":"10.1103/physreva.91.023421","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"issn":["1050-2947"],"eissn":["1094-1622"]},"year":"2015","publication_status":"published","publisher":"American Physical Society","author":[{"full_name":"Zhang, Song Bin","last_name":"Zhang","first_name":"Song Bin"},{"full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Kraus, Peter M.","first_name":"Peter M.","last_name":"Kraus"},{"last_name":"Wörner","first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob"},{"full_name":"Rohringer, Nina","last_name":"Rohringer","first_name":"Nina"}],"date_updated":"2023-08-22T08:56:34Z","date_created":"2023-08-10T06:38:10Z","volume":91,"article_number":"023421","extern":"1","publication":"Physical Review A","citation":{"ista":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. 2015. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 91(2), 023421.","apa":"Zhang, S. B., Baykusheva, D. R., Kraus, P. M., Wörner, H. J., & Rohringer, N. (2015). Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.91.023421","ieee":"S. B. Zhang, D. R. Baykusheva, P. M. Kraus, H. J. Wörner, and N. Rohringer, “Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation,” Physical Review A, vol. 91, no. 2. American Physical Society, 2015.","ama":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 2015;91(2). doi:10.1103/physreva.91.023421","chicago":"Zhang, Song Bin, Denitsa Rangelova Baykusheva, Peter M. Kraus, Hans Jakob Wörner, and Nina Rohringer. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” Physical Review A. American Physical Society, 2015. https://doi.org/10.1103/physreva.91.023421.","mla":"Zhang, Song Bin, et al. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” Physical Review A, vol. 91, no. 2, 023421, American Physical Society, 2015, doi:10.1103/physreva.91.023421.","short":"S.B. Zhang, D.R. Baykusheva, P.M. Kraus, H.J. Wörner, N. Rohringer, Physical Review A 91 (2015)."},"article_type":"original","date_published":"2015-02-19T00:00:00Z","scopus_import":"1","keyword":["Atomic and Molecular Physics","and Optics"],"day":"19","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14017","status":"public","title":"Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation","intvolume":" 91","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The detection of electron motion and electronic wave-packet dynamics is one of the core goals of attosecond science. Recently, choosing the nitric oxide molecule as an example, we have introduced and demonstrated an experimental approach to measure coupled valence electronic and rotational wave packets using high-order-harmonic-generation (HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short outline of the theory to describe the combination of the pump and HHG probe process was published together with an extensive discussion of experimental results [Baykusheva et al., Faraday Discuss. 171, 113 (2014)]. The comparison of theory and experiment showed good agreement on a quantitative level. Here, we present the theory in detail, which is based on a generalized density-matrix approach that describes the pump process and the subsequent probing of the wave packets by a semiclassical quantitative rescattering approach. An in-depth analysis of the different Raman scattering contributions to the creation of the coupled rotational and electronic spin-orbit wave packets is made. We present results for parallel and perpendicular linear polarizations of the pump and probe laser pulses. Furthermore, an analysis of the combined rotational-electronic density matrix in terms of irreducible components is presented that facilitates interpretation of the results.","lang":"eng"}],"issue":"2"},{"day":"05","article_processing_charge":"No","scopus_import":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"date_published":"2015-05-05T00:00:00Z","publication":"Nature Communications","citation":{"mla":"Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications, vol. 6, 7039, Springer Nature, 2015, doi:10.1038/ncomms8039.","short":"P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider, C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications 6 (2015).","chicago":"Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan, J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J. Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms8039.","ama":"Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 2015;6. doi:10.1038/ncomms8039","ista":"Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 6, 7039.","ieee":"P. M. Kraus et al., “Observation of laser-induced electronic structure in oriented polyatomic molecules,” Nature Communications, vol. 6. Springer Nature, 2015.","apa":"Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider, J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms8039"},"article_type":"original","abstract":[{"lang":"eng","text":"All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies."}],"type":"journal_article","oa_version":"Published Version","_id":"14016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Observation of laser-induced electronic structure in oriented polyatomic molecules","status":"public","intvolume":" 6","month":"05","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/ncomms8039","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["25940229"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms8039"}],"quality_controlled":"1","extern":"1","article_number":"7039","author":[{"full_name":"Kraus, P. M.","last_name":"Kraus","first_name":"P. M."},{"full_name":"Tolstikhin, O. I.","first_name":"O. I.","last_name":"Tolstikhin"},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"first_name":"A.","last_name":"Rupenyan","full_name":"Rupenyan, A."},{"last_name":"Schneider","first_name":"J.","full_name":"Schneider, J."},{"first_name":"C. Z.","last_name":"Bisgaard","full_name":"Bisgaard, C. Z."},{"last_name":"Morishita","first_name":"T.","full_name":"Morishita, T."},{"first_name":"F.","last_name":"Jensen","full_name":"Jensen, F."},{"first_name":"L. B.","last_name":"Madsen","full_name":"Madsen, L. B."},{"full_name":"Wörner, H. J.","first_name":"H. J.","last_name":"Wörner"}],"date_created":"2023-08-10T06:38:01Z","date_updated":"2023-08-22T08:52:56Z","volume":6,"year":"2015","pmid":1,"publication_status":"published","publisher":"Springer Nature"}]