[{"title":"Strategy complexity of finite-horizon Markov decision processes and simple stochastic games","_id":"19995","date_created":"2025-07-10T14:08:49Z","status":"public","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"type":"conference","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Markov decision processes (MDPs) and simple stochastic games (SSGs) provide a rich mathematical framework to study many important problems related to probabilistic systems. MDPs and SSGs with finite-horizon objectives, where the goal is to maximize the probability to reach a target state in a given finite time, is a classical and well-studied problem. In this work we consider the strategy complexity of finite-horizon MDPs and SSGs. We show that for all ε > 0, the natural class of counter-based strategies require at most log log/(1/ε) + n + 1 memory states, and memory of size Omega(log log(1/ε) + n) is required, for ε-optimality, where n is the number of states of the MDP (resp. SSG). Thus our bounds are asymptotically optimal. We then study the periodic property of optimal strategies, and show a sub-exponential lower bound on the period for optimal strategies."}],"citation":{"chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of Finite-Horizon Markov Decision Processes and Simple Stochastic Games.” In <i>Mathematical and Engineering Methods in Computer Science</i>, 7721:106–17. Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">https://doi.org/10.1007/978-3-642-36046-6_11</a>.","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2013). Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. In <i>Mathematical and Engineering Methods in Computer Science</i> (Vol. 7721, pp. 106–117). Znojmo, Czech Republic: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">https://doi.org/10.1007/978-3-642-36046-6_11</a>","ama":"Chatterjee K, Ibsen-Jensen R. Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. In: <i>Mathematical and Engineering Methods in Computer Science</i>. Vol 7721. Springer Nature; 2013:106-117. doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">10.1007/978-3-642-36046-6_11</a>","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of Finite-Horizon Markov Decision Processes and Simple Stochastic Games.” <i>Mathematical and Engineering Methods in Computer Science</i>, vol. 7721, Springer Nature, 2013, pp. 106–17, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">10.1007/978-3-642-36046-6_11</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Mathematical and Engineering Methods in Computer Science, Springer Nature, 2013, pp. 106–117.","ista":"Chatterjee K, Ibsen-Jensen R. 2013. Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. Mathematical and Engineering Methods in Computer Science. MEMICS: Mathematical and Engineering Methods in Computer Science, LNCS, vol. 7721, 106–117.","ieee":"K. Chatterjee and R. Ibsen-Jensen, “Strategy complexity of finite-horizon Markov decision processes and simple stochastic games,” in <i>Mathematical and Engineering Methods in Computer Science</i>, Znojmo, Czech Republic, 2013, vol. 7721, pp. 106–117."},"page":"106-117","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"date_updated":"2025-09-23T09:24:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Mathematical and Engineering Methods in Computer Science","scopus_import":"1","ec_funded":1,"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783642360466"],"isbn":["9783642360442"]},"acknowledgement":"Work of the second author supported by the Sino-Danish Center for the Theory of Interactive Computation, funded by the Danish National Research Foundation and the National Science Foundation of China (under the grant 61061130540). The second author acknowledge support from the Center for research in the Foundations of Electronic Markets (CFEM), supported by the Danish Strategic Research Council. The first author was supported by FWF Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","OA_type":"green","OA_place":"repository","language":[{"iso":"eng"}],"publication_status":"published","year":"2013","quality_controlled":"1","intvolume":"      7721","conference":{"location":"Znojmo, Czech Republic","start_date":"2012-10-25","end_date":"2012-10-28","name":"MEMICS: Mathematical and Engineering Methods in Computer Science"},"alternative_title":["LNCS"],"date_published":"2013-01-17T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1007/978-3-642-36046-6_11","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1209.3617","open_access":"1"}],"arxiv":1,"day":"17","corr_author":"1","oa":1,"external_id":{"arxiv":["1209.3617"]},"publisher":"Springer Nature","month":"01","department":[{"_id":"KrCh"}],"volume":7721,"doi":"10.1007/978-3-642-36046-6_11"},{"fulldoi":"https://doi.org/10.29012/jpc.v5i1.629","main_file_link":[{"url":"http://repository.cmu.edu/jpc/vol5/iss1/6","open_access":"1"}],"date_published":"2013-08-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","year":"2013","quality_controlled":"1","intvolume":"         5","ddc":["000"],"volume":5,"doi":"10.29012/jpc.v5i1.629","publisher":"Carnegie Mellon University","month":"08","department":[{"_id":"CaUh"}],"day":"01","oa":1,"date_updated":"2026-06-18T18:20:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"137 - 166","citation":{"chicago":"Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University, 2013. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>.","apa":"Uhler, C., Slavkovic, A., &#38; Fienberg, S. (2013). Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>","mla":"Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1, Carnegie Mellon University, 2013, pp. 137–66, doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>.","ama":"Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. 2013;5(1):137-166. doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>","ieee":"C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing for genome-wide association studies,” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013.","short":"C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality  5 (2013) 137–166.","ista":"Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 5(1), 137–166."},"type":"journal_article","oa_version":"Published Version","abstract":[{"text":"Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression.","lang":"eng"}],"title":"Privacy-preserving data sharing for genome-wide association studies","_id":"2009","author":[{"first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline"},{"first_name":"Aleksandra","last_name":"Slavkovic","full_name":"Slavkovic, Aleksandra"},{"first_name":"Stephen","last_name":"Fienberg","full_name":"Fienberg, Stephen"}],"status":"public","date_created":"2018-12-11T11:55:11Z","publist_id":"5067","language":[{"iso":"eng"}],"publication":"Journal of Privacy and Confidentiality ","issue":"1"},{"intvolume":"        41","year":"2013","quality_controlled":"1","publication_status":"published","ddc":["500"],"arxiv":1,"main_file_link":[{"url":"www.doi.org/10.1214/12-AOS1080","open_access":"1"}],"fulldoi":"https://doi.org/10.1214/12-AOS1080","article_processing_charge":"No","date_published":"2013-04-01T00:00:00Z","month":"04","department":[{"_id":"CaUh"}],"publisher":"Institute of Mathematical Statistics","external_id":{"isi":["000320488200002"],"arxiv":["1207.0547"]},"oa":1,"day":"01","doi":"10.1214/12-AOS1080","volume":41,"isi":1,"abstract":[{"lang":"eng","text":"Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case."}],"oa_version":"Published Version","type":"journal_article","status":"public","author":[{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline"},{"full_name":"Raskutti, Garvesh","last_name":"Raskutti","first_name":"Garvesh"},{"full_name":"Bühlmann, Peter","last_name":"Bühlmann","first_name":"Peter"},{"first_name":"Bin","last_name":"Yu","full_name":"Yu, Bin"}],"date_created":"2018-12-11T11:55:11Z","_id":"2010","title":"Geometry of the faithfulness assumption in causal inference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-18T18:20:45Z","page":"436 - 463","citation":{"chicago":"Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>. Institute of Mathematical Statistics, 2013. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>.","apa":"Uhler, C., Raskutti, G., Bühlmann, P., &#38; Yu, B. (2013). Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>","mla":"Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>, vol. 41, no. 2, Institute of Mathematical Statistics, 2013, pp. 436–63, doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>.","ama":"Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. 2013;41(2):436-463. doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>","ista":"Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 41(2), 436–463.","ieee":"C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness assumption in causal inference,” <i>The Annals of Statistics</i>, vol. 41, no. 2. Institute of Mathematical Statistics, pp. 436–463, 2013.","short":"C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463."},"issue":"2","scopus_import":"1","publication":"The Annals of Statistics","publist_id":"5066","language":[{"iso":"eng"}]},{"date_updated":"2021-01-12T06:55:08Z","fulldoi":"https://doi.org/10.1073/pnas.1217027110","page":"6453 - 6458","citation":{"mla":"Vicoso, Beatriz, et al. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>, vol. 110, no. 16, National Academy of Sciences, 2013, pp. 6453–58, doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>.","ama":"Vicoso B, Kaiser V, Bachtrog D. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. 2013;110(16):6453-6458. doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>","ista":"Vicoso B, Kaiser V, Bachtrog D. 2013. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. 110(16), 6453–6458.","short":"B. Vicoso, V. Kaiser, D. Bachtrog, PNAS 110 (2013) 6453–6458.","ieee":"B. Vicoso, V. Kaiser, and D. Bachtrog, “Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution,” <i>PNAS</i>, vol. 110, no. 16. National Academy of Sciences, pp. 6453–6458, 2013.","chicago":"Vicoso, Beatriz, Vera Kaiser, and Doris Bachtrog. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>.","apa":"Vicoso, B., Kaiser, V., &#38; Bachtrog, D. (2013). Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>"},"date_published":"2013-04-16T00:00:00Z","intvolume":"       110","extern":1,"abstract":[{"text":"Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes. ","lang":"eng"}],"type":"journal_article","publication_status":"published","quality_controlled":0,"year":"2013","author":[{"orcid":"0000-0002-4579-8306","full_name":"Beatriz Vicoso","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaiser","first_name":"Vera","full_name":"Kaiser, Vera B"},{"last_name":"Bachtrog","first_name":"Doris","full_name":"Bachtrog, Doris"}],"date_created":"2018-12-11T11:55:33Z","status":"public","title":"Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution","_id":"2074","doi":"10.1073/pnas.1217027110","volume":110,"publist_id":"4964","publisher":"National Academy of Sciences","month":"04","issue":"16","day":"16","publication":"PNAS"},{"citation":{"chicago":"Vicoso, Beatriz, Jr Emerson, Yulia Zektser, Shivani Mahajan, and Doris Bachtrog. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>.","apa":"Vicoso, B., Emerson, J., Zektser, Y., Mahajan, S., &#38; Bachtrog, D. (2013). Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>","mla":"Vicoso, Beatriz, et al. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>, vol. 11, no. 8, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>.","ama":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. 2013;11(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>","ieee":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog, “Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation,” <i>PLoS Biology</i>, vol. 11, no. 8. Public Library of Science, 2013.","ista":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. 2013. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. 11(8).","short":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, D. Bachtrog, PLoS Biology 11 (2013)."},"date_published":"2013-08-27T00:00:00Z","date_updated":"2021-01-12T06:55:09Z","fulldoi":"https://doi.org/10.1371/journal.pbio.1001643","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2018-12-11T11:55:34Z","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Beatriz Vicoso","orcid":"0000-0002-4579-8306"},{"full_name":"Emerson, Jr J.","first_name":"Jr","last_name":"Emerson"},{"full_name":"Zektser, Yulia","first_name":"Yulia","last_name":"Zektser"},{"full_name":"Mahajan, Shivani","last_name":"Mahajan","first_name":"Shivani"},{"full_name":"Bachtrog, Doris","first_name":"Doris","last_name":"Bachtrog"}],"status":"public","title":"Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation","_id":"2076","intvolume":"        11","abstract":[{"text":"Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.\n","lang":"eng"}],"extern":1,"type":"journal_article","publication_status":"published","year":"2013","quality_controlled":0,"doi":"10.1371/journal.pbio.1001643","volume":11,"publist_id":"4962","issue":"8","day":"27","publication":"PLoS Biology","publisher":"Public Library of Science","month":"08","acknowledgement":"Funded by NIH grants (R01GM076007 and R01GM093182) and a Packard Fellowship to DB."},{"date_updated":"2021-11-29T14:05:19Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Mognetti, B. M., Anđela Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/physrevlett.111.245702\">https://doi.org/10.1103/physrevlett.111.245702</a>.","apa":"Mognetti, B. M., Šarić, A., Angioletti-Uberti, S., Cacciuto, A., Valeriani, C., &#38; Frenkel, D. (2013). Living clusters and crystals from low-density suspensions of active colloids. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.111.245702\">https://doi.org/10.1103/physrevlett.111.245702</a>","ama":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. Living clusters and crystals from low-density suspensions of active colloids. <i>Physical Review Letters</i>. 2013;111(24). doi:<a href=\"https://doi.org/10.1103/physrevlett.111.245702\">10.1103/physrevlett.111.245702</a>","mla":"Mognetti, B. M., et al. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” <i>Physical Review Letters</i>, vol. 111, no. 24, 245702, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/physrevlett.111.245702\">10.1103/physrevlett.111.245702</a>.","short":"B.M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, D. Frenkel, Physical Review Letters 111 (2013).","ieee":"B. M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel, “Living clusters and crystals from low-density suspensions of active colloids,” <i>Physical Review Letters</i>, vol. 111, no. 24. American Physical Society, 2013.","ista":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. 2013. Living clusters and crystals from low-density suspensions of active colloids. Physical Review Letters. 111(24), 245702."},"type":"journal_article","oa_version":"Preprint","article_type":"original","abstract":[{"text":"Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.","lang":"eng"}],"extern":"1","title":"Living clusters and crystals from low-density suspensions of active colloids","_id":"10384","author":[{"full_name":"Mognetti, B. M.","last_name":"Mognetti","first_name":"B. M."},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"},{"last_name":"Angioletti-Uberti","first_name":"S.","full_name":"Angioletti-Uberti, S."},{"first_name":"A.","last_name":"Cacciuto","full_name":"Cacciuto, A."},{"last_name":"Valeriani","first_name":"C.","full_name":"Valeriani, C."},{"first_name":"D.","last_name":"Frenkel","full_name":"Frenkel, D."}],"status":"public","date_created":"2021-11-29T13:29:31Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"acknowledgement":"This work was supported by the ERC Advanced Grant 227758, the National Science Foundation under Career Grant No. DMR-0846426, the Wolfson Merit Award 2007/R3 of the Royal Society of London and the EPSRC Programme Grant EP/I001352/1. BMM acknowledge T. Curk and A. Ballard for useful discussions. C. V. acknowledges financial support from a Juan de la Cierva Fellowship, from the Marie Curie Integration Grant PCIG-GA-2011-303941 ANISOKINEQ, and from the National Project FIS2010- 16159. S. A-U acknowledges support from the Alexander von Humboldt Foundation.","publication":"Physical Review Letters","scopus_import":"1","issue":"24","fulldoi":"https://doi.org/10.1103/physrevlett.111.245702","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.4681"}],"arxiv":1,"date_published":"2013-12-11T00:00:00Z","article_processing_charge":"No","keyword":["general physics and astronomy"],"publication_status":"published","year":"2013","quality_controlled":"1","pmid":1,"intvolume":"       111","volume":111,"doi":"10.1103/physrevlett.111.245702","article_number":"245702","external_id":{"pmid":["24483677"],"arxiv":["1311.4681"]},"publisher":"American Physical Society","month":"12","day":"11","oa":1},{"publication":"Soft Matter","scopus_import":"1","issue":"37","acknowledgement":"This work was supported by the National Science Foundation under Career Grant no. DMR-0846426.","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"language":[{"iso":"eng"}],"title":"Collapsing nanoparticle-laden nanotubes","_id":"10385","author":[{"first_name":"Joseph A.","last_name":"Napoli","full_name":"Napoli, Joseph A."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Cacciuto, Angelo","last_name":"Cacciuto","first_name":"Angelo"}],"date_created":"2021-11-29T13:31:24Z","status":"public","type":"journal_article","oa_version":"None","article_type":"original","extern":"1","abstract":[{"text":"We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials.","lang":"eng"}],"citation":{"ista":"Napoli JA, Šarić A, Cacciuto A. 2013. Collapsing nanoparticle-laden nanotubes. Soft Matter. 9(37), 8881–8886.","short":"J.A. Napoli, A. Šarić, A. Cacciuto, Soft Matter 9 (2013) 8881–8886.","ieee":"J. A. Napoli, A. Šarić, and A. Cacciuto, “Collapsing nanoparticle-laden nanotubes,” <i>Soft Matter</i>, vol. 9, no. 37. Royal Society of Chemistry, pp. 8881–8886, 2013.","ama":"Napoli JA, Šarić A, Cacciuto A. Collapsing nanoparticle-laden nanotubes. <i>Soft Matter</i>. 2013;9(37):8881-8886. doi:<a href=\"https://doi.org/10.1039/c3sm51495a\">10.1039/c3sm51495a</a>","mla":"Napoli, Joseph A., et al. “Collapsing Nanoparticle-Laden Nanotubes.” <i>Soft Matter</i>, vol. 9, no. 37, Royal Society of Chemistry, 2013, pp. 8881–86, doi:<a href=\"https://doi.org/10.1039/c3sm51495a\">10.1039/c3sm51495a</a>.","apa":"Napoli, J. A., Šarić, A., &#38; Cacciuto, A. (2013). Collapsing nanoparticle-laden nanotubes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm51495a\">https://doi.org/10.1039/c3sm51495a</a>","chicago":"Napoli, Joseph A., Anđela Šarić, and Angelo Cacciuto. “Collapsing Nanoparticle-Laden Nanotubes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm51495a\">https://doi.org/10.1039/c3sm51495a</a>."},"page":"8881-8886","date_updated":"2021-11-29T14:05:23Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"08","publisher":"Royal Society of Chemistry","month":"08","volume":9,"doi":"10.1039/c3sm51495a","publication_status":"published","year":"2013","quality_controlled":"1","intvolume":"         9","date_published":"2013-08-08T00:00:00Z","article_processing_charge":"No","keyword":["condensed matter physics","general chemistry"],"fulldoi":"https://doi.org/10.1039/c3sm51495a"},{"intvolume":"         9","publication_status":"published","quality_controlled":"1","year":"2013","article_processing_charge":"No","keyword":["condensed matter physics","general chemistry"],"date_published":"2013-05-03T00:00:00Z","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2013/sm/c3sm50188d"}],"fulldoi":"https://doi.org/10.1039/c3sm50188d","day":"03","publisher":"Royal Society of Chemistry","month":"05","article_number":"6677","doi":"10.1039/c3sm50188d","volume":9,"author":[{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Cacciuto, Angelo","first_name":"Angelo","last_name":"Cacciuto"}],"status":"public","date_created":"2021-11-29T14:06:32Z","title":"Self-assembly of nanoparticles adsorbed on fluid and elastic membranes","_id":"10386","extern":"1","abstract":[{"lang":"eng","text":"In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface."}],"type":"journal_article","oa_version":"None","article_type":"original","citation":{"chicago":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm50188d\">https://doi.org/10.1039/c3sm50188d</a>.","apa":"Šarić, A., &#38; Cacciuto, A. (2013). Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm50188d\">https://doi.org/10.1039/c3sm50188d</a>","ama":"Šarić A, Cacciuto A. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. <i>Soft Matter</i>. 2013;9(29). doi:<a href=\"https://doi.org/10.1039/c3sm50188d\">10.1039/c3sm50188d</a>","mla":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” <i>Soft Matter</i>, vol. 9, no. 29, 6677, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3sm50188d\">10.1039/c3sm50188d</a>.","ieee":"A. Šarić and A. Cacciuto, “Self-assembly of nanoparticles adsorbed on fluid and elastic membranes,” <i>Soft Matter</i>, vol. 9, no. 29. Royal Society of Chemistry, 2013.","short":"A. Šarić, A. Cacciuto, Soft Matter 9 (2013).","ista":"Šarić A, Cacciuto A. 2013. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 9(29), 6677."},"date_updated":"2021-11-29T14:29:31Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","issue":"29","publication":"Soft Matter","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR 0846426. The authors thank J. C. Pàmies for many fruitful discussions on the subject.","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"language":[{"iso":"eng"}]},{"fulldoi":"https://doi.org/10.1515/bmt-2013-4181","article_processing_charge":"No","keyword":["biomedical engineering","data analysis","free software"],"has_accepted_license":"1","conference":{"end_date":"2013-09-21","start_date":"2013-09-19","name":"BMT: Biomedizinische Technik ","location":"Graz, Austria"},"file_date_updated":"2021-12-01T14:38:08Z","date_published":"2013-08-01T00:00:00Z","intvolume":"        58","publication_status":"published","pmid":1,"quality_controlled":"1","year":"2013","ddc":["005","610"],"doi":"10.1515/bmt-2013-4181","file":[{"access_level":"open_access","creator":"schloegl","relation":"main_file","success":1,"date_created":"2021-12-01T14:38:08Z","checksum":"cdfc5339b530a25d6079f7223f0b1f16","file_name":"Schloegl_Abstract-BMT2013.pdf","content_type":"application/pdf","date_updated":"2021-12-01T14:38:08Z","file_size":149825,"file_id":"10397"}],"volume":58,"isi":1,"article_number":"000010151520134181","publisher":"De Gruyter","month":"08","department":[{"_id":"PeJo"}],"external_id":{"pmid":["24042795"],"isi":["000497714000034"]},"oa":1,"corr_author":"1","day":"01","date_updated":"2025-09-30T07:31:23Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.","short":"A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013).","ieee":"A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A fast visualization and analysis environment for cellular neurophysiology,” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G. De Gruyter, 2013.","ama":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. 2013;58(SI-1-Track-G). doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>","mla":"Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>.","apa":"Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., &#38; Guzman, S. J. (2013). Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. Graz, Austria: De Gruyter. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>","chicago":"Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>. De Gruyter, 2013. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>."},"abstract":[{"lang":"eng","text":"Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable."}],"oa_version":"Submitted Version","type":"journal_article","article_type":"original","author":[{"first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"full_name":"Schmidt-Hieber, C.","first_name":"C.","last_name":"Schmidt-Hieber"},{"last_name":"Guzman","first_name":"S. J.","full_name":"Guzman, S. J."}],"status":"public","date_created":"2021-12-01T14:35:35Z","title":"Stimfit: A fast visualization and analysis environment for cellular neurophysiology","_id":"10396","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0013-5585"],"eissn":["1862-278X"]},"issue":"SI-1-Track-G","publication":"Biomedical Engineering / Biomedizinische Technik"},{"volume":58,"article_number":"N36.00001","month":"03","publisher":"American Physical Society","day":"01","oa":1,"main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR13/Event/186873","open_access":"1"}],"alternative_title":["Bulletin of the American Physical Society"],"date_published":"2013-03-01T00:00:00Z","conference":{"location":"Baltimore, MD, United States","start_date":"2013-03-18","end_date":"2013-03-22","name":"APS: American Physical Society"},"article_processing_charge":"No","year":"2013","quality_controlled":"1","publication_status":"published","intvolume":"        58","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the Center for Emergent Superconductivity, an Energy Frontier Research Center funded by the US DOE, Office of Science.","publication_identifier":{"issn":["0003-0503"]},"publication":"APS March Meeting 2013","issue":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-02-08T10:48:06Z","citation":{"chicago":"Polshyn, Hryhoriy, Raffi Budakian, and Genda Gu. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” In <i>APS March Meeting 2013</i>, Vol. 58. American Physical Society, 2013.","apa":"Polshyn, H., Budakian, R., &#38; Gu, G. (2013). Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In <i>APS March Meeting 2013</i> (Vol. 58). Baltimore, MD, United States: American Physical Society.","ama":"Polshyn H, Budakian R, Gu G. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In: <i>APS March Meeting 2013</i>. Vol 58. American Physical Society; 2013.","mla":"Polshyn, Hryhoriy, et al. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” <i>APS March Meeting 2013</i>, vol. 58, no. 1, N36.00001, American Physical Society, 2013.","ista":"Polshyn H, Budakian R, Gu G. 2013. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. APS March Meeting 2013. APS: American Physical Society, Bulletin of the American Physical Society, vol. 58, N36.00001.","ieee":"H. Polshyn, R. Budakian, and G. Gu, “Cantilever micro-susceptometry of mesoscopic Bi2212 samples,” in <i>APS March Meeting 2013</i>, Baltimore, MD, United States, 2013, vol. 58, no. 1.","short":"H. Polshyn, R. Budakian, G. Gu, in:, APS March Meeting 2013, American Physical Society, 2013."},"type":"conference","oa_version":"Published Version","extern":"1","abstract":[{"lang":"eng","text":"Fluxoid quantization provides a direct means to study phase coherence. In cuprate superconductors, there have been observations which suggest that phase coherent superconducting fluctuations may persist at temperatures significantly above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate superconducting samples to directly probe phase coherence over a wide range of temperatures. We present cantilever torque susceptometry measurements of micron and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique allowed observation of transitions between different fluxoid states of a single ring, and the discrete vortex states of micron size disks. The dependence of magnetic susceptibility on diameter and wall thickness of the ring was investigated. Measurements were made at different values of the in-plane magnetic field, and over a wide range of temperatures."}],"_id":"10749","title":"Cantilever micro-susceptometry of mesoscopic Bi2212 samples","author":[{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy","last_name":"Polshyn"},{"first_name":"Raffi","last_name":"Budakian","full_name":"Budakian, Raffi"},{"full_name":"Gu, Genda","first_name":"Genda","last_name":"Gu"}],"date_created":"2022-02-08T10:34:29Z","status":"public"},{"page":"549-560","citation":{"mla":"Tang, Yong, et al. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” <i>Acta Biochimica et Biophysica Sinica</i>, vol. 45, no. 7, Oxford University Press, 2013, pp. 549–60, doi:<a href=\"https://doi.org/10.1093/abbs/gmt039\">10.1093/abbs/gmt039</a>.","ama":"Tang Y, Tan S, Xue H. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. <i>Acta Biochimica et Biophysica Sinica</i>. 2013;45(7):549-560. doi:<a href=\"https://doi.org/10.1093/abbs/gmt039\">10.1093/abbs/gmt039</a>","ieee":"Y. Tang, S. Tan, and H. Xue, “Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development,” <i>Acta Biochimica et Biophysica Sinica</i>, vol. 45, no. 7. Oxford University Press, pp. 549–560, 2013.","ista":"Tang Y, Tan S, Xue H. 2013. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 45(7), 549–560.","short":"Y. Tang, S. Tan, H. Xue, Acta Biochimica et Biophysica Sinica 45 (2013) 549–560.","chicago":"Tang, Yong, Shutang Tan, and Hongwei Xue. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” <i>Acta Biochimica et Biophysica Sinica</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/abbs/gmt039\">https://doi.org/10.1093/abbs/gmt039</a>.","apa":"Tang, Y., Tan, S., &#38; Xue, H. (2013). Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. <i>Acta Biochimica et Biophysica Sinica</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/abbs/gmt039\">https://doi.org/10.1093/abbs/gmt039</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:14:23Z","date_created":"2020-03-21T16:06:36Z","status":"public","author":[{"last_name":"Tang","first_name":"Yong","full_name":"Tang, Yong"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xue, Hongwei","last_name":"Xue","first_name":"Hongwei"}],"_id":"7595","title":"Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development","abstract":[{"lang":"eng","text":"Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK) phosphorylates inositol 1,3,4-trisphosphate to form inositol 1,3,4,5-tetrakisphosphate and inositol 1,3,4,6-tetrakisphosphate which can be finally transferred to inositol hexaphosphate (IP6) and play important roles during plant growth and development. There are 4 putative ITPK members in Arabidopsis. Expression pattern analysis showed that ITPK2 is constitutively expressed in various tissues. A T-DNA knockout mutant of ITPK2 was identified and scanning electron microscopy (SEM) analysis showed that the epidermis structure of seed coat was irregularly formed in seeds of itpk2-1 mutant, resulting in the increased permeability of seed coat to tetrazolium salts. Further analysis by gas chromatography coupled with mass spectrometry of lipid polyester monomers in cell wall confirmed a dramatic decrease in composition of suberin and cutin, which relate to the permeability of seed coat and the formation of which is accompanied with seed coat development. These results indicate that ITPK2 plays an essential role in seed coat development and lipid polyester barrier formation."}],"extern":"1","article_type":"original","type":"journal_article","oa_version":"None","language":[{"iso":"eng"}],"issue":"7","publication":"Acta Biochimica et Biophysica Sinica","publication_identifier":{"issn":["1745-7270","1672-9145"]},"article_processing_charge":"No","date_published":"2013-07-01T00:00:00Z","fulldoi":"https://doi.org/10.1093/abbs/gmt039","intvolume":"        45","year":"2013","quality_controlled":"1","pmid":1,"publication_status":"published","doi":"10.1093/abbs/gmt039","volume":45,"day":"01","month":"07","publisher":"Oxford University Press","external_id":{"pmid":["23595027"]}},{"fulldoi":"https://doi.org/10.1105/tpc.113.114322","date_published":"2013-08-26T00:00:00Z","article_processing_charge":"No","year":"2013","pmid":1,"quality_controlled":"1","publication_status":"published","intvolume":"        25","volume":25,"doi":"10.1105/tpc.113.114322","external_id":{"pmid":["23897926"]},"month":"08","publisher":"American Society of Plant Biologists","day":"26","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:14:24Z","citation":{"ama":"Tan S, Dai C, Liu H-T, Xue H-W. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. <i>The Plant Cell</i>. 2013;25(7):2618-2632. doi:<a href=\"https://doi.org/10.1105/tpc.113.114322\">10.1105/tpc.113.114322</a>","mla":"Tan, Shutang, et al. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” <i>The Plant Cell</i>, vol. 25, no. 7, American Society of Plant Biologists, 2013, pp. 2618–32, doi:<a href=\"https://doi.org/10.1105/tpc.113.114322\">10.1105/tpc.113.114322</a>.","ieee":"S. Tan, C. Dai, H.-T. Liu, and H.-W. Xue, “Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling,” <i>The Plant Cell</i>, vol. 25, no. 7. American Society of Plant Biologists, pp. 2618–2632, 2013.","short":"S. Tan, C. Dai, H.-T. Liu, H.-W. Xue, The Plant Cell 25 (2013) 2618–2632.","ista":"Tan S, Dai C, Liu H-T, Xue H-W. 2013. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. 25(7), 2618–2632.","chicago":"Tan, Shutang, C. Dai, H.-T. Liu, and H.-W. Xue. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” <i>The Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114322\">https://doi.org/10.1105/tpc.113.114322</a>.","apa":"Tan, S., Dai, C., Liu, H.-T., &#38; Xue, H.-W. (2013). Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. <i>The Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114322\">https://doi.org/10.1105/tpc.113.114322</a>"},"page":"2618-2632","article_type":"original","type":"journal_article","oa_version":"None","abstract":[{"lang":"eng","text":"Casein kinase1 (CK1) plays crucial roles in regulating growth and development via phosphorylating various substrates throughout the eukaryote kingdom. Blue light is crucial for normal growth of both plants and animals, and blue light receptor cryptochrome2 (CRY2) undergoes blue light–dependent phosphorylation and degradation in planta. To study the function of plant CK1s, systematic genetic analysis showed that deficiency of two paralogous Arabidopsis thaliana CK1s, CK1.3 and CK1.4, caused shortened hypocotyls, especially under blue light, while overexpression of either CK1.3 or CK1.4 resulted in the insensitive response to blue light and delayed flowering under long-day conditions. CK1.3 or CK1.4 act dependently on CRY2, and overexpression of CK1.3 or CK1.4 significantly suppresses the hypersensitive response to blue light by CRY2 overexpression. Biochemical studies showed that CK1.3 and CK1.4 directly phosphorylate CRY2 at Ser-587 and Thr-603 in vitro and negatively regulate CRY2 stability in planta, which are stimulated by blue light, further confirming the crucial roles of CK1.3 and CK1.4 in blue light responses through phosphorylating CRY2. Interestingly, expression of CK1.3 and CK1.4 is stimulated by blue light and feedback regulated by CRY2-mediated signaling. These results provide direct evidence for CRY2 phosphorylation and informative clues on the mechanisms of CRY2-mediated light responses."}],"extern":"1","_id":"7596","title":"Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling","author":[{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang"},{"full_name":"Dai, C.","last_name":"Dai","first_name":"C."},{"full_name":"Liu, H.-T.","last_name":"Liu","first_name":"H.-T."},{"last_name":"Xue","first_name":"H.-W.","full_name":"Xue, H.-W."}],"date_created":"2020-03-21T16:06:55Z","status":"public","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1040-4651","1532-298X"]},"publication":"The Plant Cell","issue":"7"},{"conference":{"name":"PODC: Principles of Distributed Computing"},"date_published":"2013-01-01T00:00:00Z","page":"200 - 209","citation":{"ieee":"D.-A. Alistarh, J. Aspnes, G. Giakkoupis, and P. Woelfel, “Randomized loose renaming in O(loglogn) time,” presented at the PODC: Principles of Distributed Computing, 2013, pp. 200–209.","short":"D.-A. Alistarh, J. Aspnes, G. Giakkoupis, P. Woelfel, in:, ACM, 2013, pp. 200–209.","ista":"Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. 2013. Randomized loose renaming in O(loglogn) time. PODC: Principles of Distributed Computing, 200–209.","ama":"Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. Randomized loose renaming in O(loglogn) time. In: ACM; 2013:200-209. doi:<a href=\"https://doi.org/10.1145/2484239.2484240\">10.1145/2484239.2484240</a>","mla":"Alistarh, Dan-Adrian, et al. <i>Randomized Loose Renaming in O(Loglogn) Time</i>. ACM, 2013, pp. 200–09, doi:<a href=\"https://doi.org/10.1145/2484239.2484240\">10.1145/2484239.2484240</a>.","apa":"Alistarh, D.-A., Aspnes, J., Giakkoupis, G., &#38; Woelfel, P. (2013). Randomized loose renaming in O(loglogn) time (pp. 200–209). Presented at the PODC: Principles of Distributed Computing, ACM. <a href=\"https://doi.org/10.1145/2484239.2484240\">https://doi.org/10.1145/2484239.2484240</a>","chicago":"Alistarh, Dan-Adrian, James Aspnes, George Giakkoupis, and Philipp Woelfel. “Randomized Loose Renaming in O(Loglogn) Time,” 200–209. ACM, 2013. <a href=\"https://doi.org/10.1145/2484239.2484240\">https://doi.org/10.1145/2484239.2484240</a>."},"article_processing_charge":"No","date_updated":"2023-02-23T13:13:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1145/2484239.2484240","title":"Randomized loose renaming in O(loglogn) time","_id":"765","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Aspnes, James","first_name":"James","last_name":"Aspnes"},{"full_name":"Giakkoupis, George","first_name":"George","last_name":"Giakkoupis"},{"full_name":"Woelfel, Philipp","first_name":"Philipp","last_name":"Woelfel"}],"status":"public","date_created":"2018-12-11T11:48:23Z","type":"conference","publication_status":"published","oa_version":"None","year":"2013","abstract":[{"text":"Renaming is a classic distributed coordination task in which a set of processes must pick distinct identifiers from a small namespace. In this paper, we consider the time complexity of this problem when the namespace is linear in the number of participants, a variant known as loose renaming. We give a non-adaptive algorithm with O(log log n) (individual) step complexity, where n is a known upper bound on contention, and an adaptive algorithm with step complexity O((log log k)2), where k is the actual contention in the execution. We also present a variant of the adaptive algorithm which requires O(k log log k) total process steps. All upper bounds hold with high probability against a strong adaptive adversary. We complement the algorithms with an ω(log log n) expected time lower bound on the complexity of randomized renaming using test-and-set operations and linear space. The result is based on a new coupling technique, and is the first to apply to non-adaptive randomized renaming. Since our algorithms use O(n) test-and-set objects, our results provide matching bounds on the cost of loose renaming in this setting.","lang":"eng"}],"extern":"1","publist_id":"6889","language":[{"iso":"eng"}],"doi":"10.1145/2484239.2484240","day":"01","publisher":"ACM","month":"01","acknowledgement":"Dan Alistarh - This author was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant\r\nER26116/DE-SC0008923,  and  by  grants  from  the  Oracle\r\nand Intel corporations.\r\nJames Aspnes - Supported in part by NSF grant CCF-0916389.\r\nGeorge Giakkoupis - This work was funded in part by INRIA Associate Team\r\nRADCON, and ERC Starting Grant GOSSPLE 204742.\r\nPhilipp Woelfel - This research was undertaken, in part, thanks to funding\r\nfrom the Canada Research Chairs program and the HP Labs\r\nInnovation Research Program."},{"doi":"10.1111/mec.12375","language":[{"iso":"eng"}],"volume":22,"issue":"15","day":"01","publication":"Molecular Ecology","publication_identifier":{"issn":["0962-1083"]},"month":"08","publisher":"Wiley","article_processing_charge":"No","citation":{"short":"M.R. Robinson, A.W. Santure, I. DeCauwer, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3963–3980.","ista":"Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. 2013. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 22(15), 3963–3980.","ieee":"M. R. Robinson, A. W. Santure, I. DeCauwer, B. C. Sheldon, and J. Slate, “Partitioning of genetic variation across the genome using multimarker methods in a wild bird population,” <i>Molecular Ecology</i>, vol. 22, no. 15. Wiley, pp. 3963–3980, 2013.","ama":"Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. <i>Molecular Ecology</i>. 2013;22(15):3963-3980. doi:<a href=\"https://doi.org/10.1111/mec.12375\">10.1111/mec.12375</a>","mla":"Robinson, Matthew Richard, et al. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” <i>Molecular Ecology</i>, vol. 22, no. 15, Wiley, 2013, pp. 3963–80, doi:<a href=\"https://doi.org/10.1111/mec.12375\">10.1111/mec.12375</a>.","apa":"Robinson, M. R., Santure, A. W., DeCauwer, I., Sheldon, B. C., &#38; Slate, J. (2013). Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.12375\">https://doi.org/10.1111/mec.12375</a>","chicago":"Robinson, Matthew Richard, Anna W. Santure, Isabelle DeCauwer, Ben C. Sheldon, and Jon Slate. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” <i>Molecular Ecology</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/mec.12375\">https://doi.org/10.1111/mec.12375</a>."},"page":"3963-3980","date_published":"2013-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1111/mec.12375","date_updated":"2021-01-12T08:15:14Z","date_created":"2020-04-30T11:00:15Z","author":[{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Anna W.","last_name":"Santure","full_name":"Santure, Anna W."},{"last_name":"DeCauwer","first_name":"Isabelle","full_name":"DeCauwer, Isabelle"},{"last_name":"Sheldon","first_name":"Ben C.","full_name":"Sheldon, Ben C."},{"last_name":"Slate","first_name":"Jon","full_name":"Slate, Jon"}],"status":"public","_id":"7745","title":"Partitioning of genetic variation across the genome using multimarker methods in a wild bird population","extern":"1","abstract":[{"lang":"eng","text":"The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high‐density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex‐, age‐ and environment‐specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems."}],"intvolume":"        22","year":"2013","quality_controlled":"1","article_type":"original","publication_status":"published","type":"journal_article","oa_version":"None"},{"language":[{"iso":"eng"}],"volume":22,"doi":"10.1111/mec.12376","month":"08","publication_identifier":{"issn":["0962-1083"]},"publisher":"Wiley","publication":"Molecular Ecology","day":"01","issue":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1111/mec.12376","date_updated":"2021-01-12T08:15:14Z","date_published":"2013-08-01T00:00:00Z","article_processing_charge":"No","citation":{"chicago":"Santure, Anna W., Isabelle De Cauwer, Matthew Richard Robinson, Jocelyn Poissant, Ben C. Sheldon, and Jon Slate. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” <i>Molecular Ecology</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/mec.12376\">https://doi.org/10.1111/mec.12376</a>.","apa":"Santure, A. W., De Cauwer, I., Robinson, M. R., Poissant, J., Sheldon, B. C., &#38; Slate, J. (2013). Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.12376\">https://doi.org/10.1111/mec.12376</a>","ama":"Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. <i>Molecular Ecology</i>. 2013;22(15):3949-3962. doi:<a href=\"https://doi.org/10.1111/mec.12376\">10.1111/mec.12376</a>","mla":"Santure, Anna W., et al. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” <i>Molecular Ecology</i>, vol. 22, no. 15, Wiley, 2013, pp. 3949–62, doi:<a href=\"https://doi.org/10.1111/mec.12376\">10.1111/mec.12376</a>.","ieee":"A. W. Santure, I. De Cauwer, M. R. Robinson, J. Poissant, B. C. Sheldon, and J. Slate, “Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population,” <i>Molecular Ecology</i>, vol. 22, no. 15. Wiley, pp. 3949–3962, 2013.","short":"A.W. Santure, I. De Cauwer, M.R. Robinson, J. Poissant, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3949–3962.","ista":"Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. 2013. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. 22(15), 3949–3962."},"page":"3949-3962","quality_controlled":"1","article_type":"original","year":"2013","oa_version":"None","publication_status":"published","type":"journal_article","intvolume":"        22","abstract":[{"text":"Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade‐off between them, either at the phenotypic or at the genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker‐based approaches – chromosome partitioning, quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome‐wide significant QTL, and no individual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, nonsignificant negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait.","lang":"eng"}],"extern":"1","_id":"7746","title":"Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population","author":[{"first_name":"Anna W.","last_name":"Santure","full_name":"Santure, Anna W."},{"full_name":"De Cauwer, Isabelle","last_name":"De Cauwer","first_name":"Isabelle"},{"last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"first_name":"Jocelyn","last_name":"Poissant","full_name":"Poissant, Jocelyn"},{"last_name":"Sheldon","first_name":"Ben C.","full_name":"Sheldon, Ben C."},{"full_name":"Slate, Jon","first_name":"Jon","last_name":"Slate"}],"date_created":"2020-04-30T11:00:32Z","status":"public"},{"publication_identifier":{"issn":["1461-023X"]},"month":"03","publisher":"Wiley","day":"01","publication":"Ecology Letters","issue":"3","language":[{"iso":"eng"}],"volume":16,"doi":"10.1111/ele.12047","year":"2013","quality_controlled":"1","article_type":"original","publication_status":"published","oa_version":"None","type":"journal_article","abstract":[{"text":"Acquisition and allocation of resources are central to life‐history theory. However, empirical work typically focuses only on allocation despite the fact that relationships between fitness components may be governed by differences in the ability of individuals to acquire resources across environments. Here, we outline a statistical framework to partition the genetic basis of multivariate plasticity into independent axes of genetic variation, and quantify for the first time, the extent to which specific traits drive multitrait genotype–environment interactions. Our framework generalises to analyses of plasticity, growth and ageing. We apply this approach to a unique, large‐scale, multivariate study of acquisition, allocation and plasticity in the life history of the cricket, Gryllus firmus. We demonstrate that resource acquisition and allocation are genetically correlated, and that plasticity in trade‐offs between allocation to components of fitness is 90% dependent on genetic variance for total resource acquisition. These results suggest that genotype–environment effects for resource acquisition can maintain variation in life‐history components that are typically observed in the wild.","lang":"eng"}],"extern":"1","intvolume":"        16","_id":"7747","title":"Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history","date_created":"2020-04-30T11:00:49Z","status":"public","author":[{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"last_name":"Beckerman","first_name":"Andrew P.","full_name":"Beckerman, Andrew P."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1111/ele.12047","date_updated":"2021-01-12T08:15:15Z","date_published":"2013-03-01T00:00:00Z","citation":{"apa":"Robinson, M. R., &#38; Beckerman, A. P. (2013). Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. <i>Ecology Letters</i>. Wiley. <a href=\"https://doi.org/10.1111/ele.12047\">https://doi.org/10.1111/ele.12047</a>","chicago":"Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” <i>Ecology Letters</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/ele.12047\">https://doi.org/10.1111/ele.12047</a>.","short":"M.R. Robinson, A.P. Beckerman, Ecology Letters 16 (2013) 281–290.","ieee":"M. R. Robinson and A. P. Beckerman, “Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history,” <i>Ecology Letters</i>, vol. 16, no. 3. Wiley, pp. 281–290, 2013.","ista":"Robinson MR, Beckerman AP. 2013. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. 16(3), 281–290.","ama":"Robinson MR, Beckerman AP. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. <i>Ecology Letters</i>. 2013;16(3):281-290. doi:<a href=\"https://doi.org/10.1111/ele.12047\">10.1111/ele.12047</a>","mla":"Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” <i>Ecology Letters</i>, vol. 16, no. 3, Wiley, 2013, pp. 281–90, doi:<a href=\"https://doi.org/10.1111/ele.12047\">10.1111/ele.12047</a>."},"article_processing_charge":"No","page":"281-290"},{"doi":"10.1039/c3sm51095f","language":[{"iso":"eng"}],"volume":9,"article_number":"10993","publication_identifier":{"issn":["1744-683X","1744-6848"]},"month":"10","publisher":"Royal Society of Chemistry","issue":"46","publication":"Soft Matter","day":"08","fulldoi":"https://doi.org/10.1039/c3sm51095f","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:15:27Z","article_processing_charge":"No","citation":{"chicago":"Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability of Jammed Packings I: The Rigidity Length Scale.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm51095f\">https://doi.org/10.1039/c3sm51095f</a>.","apa":"Goodrich, C. P., Ellenbroek, W. G., &#38; Liu, A. J. (2013). Stability of jammed packings I: The rigidity length scale. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm51095f\">https://doi.org/10.1039/c3sm51095f</a>","mla":"Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity Length Scale.” <i>Soft Matter</i>, vol. 9, no. 46, 10993, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3sm51095f\">10.1039/c3sm51095f</a>.","ama":"Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity length scale. <i>Soft Matter</i>. 2013;9(46). doi:<a href=\"https://doi.org/10.1039/c3sm51095f\">10.1039/c3sm51095f</a>","ista":"Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I: The rigidity length scale. Soft Matter. 9(46), 10993.","ieee":"C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings I: The rigidity length scale,” <i>Soft Matter</i>, vol. 9, no. 46. Royal Society of Chemistry, 2013.","short":"C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013)."},"date_published":"2013-10-08T00:00:00Z","extern":"1","intvolume":"         9","abstract":[{"text":"In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low frequency vibrational properties of jammed amorphous sphere packings can be understood in terms of a length scale, called l*, that diverges as the system becomes marginally unstable. Despite the tremendous success of this theory, it has been difficult to connect the counting argument that defines l* to other length scales that diverge near the jamming transition. We present an alternate derivation of l* based on the onset of rigidity. This phenomenological approach reveals the physical mechanism underlying the length scale and is relevant to a range of systems for which the original argument breaks down. It also allows us to present the first direct numerical measurement of l*.","lang":"eng"}],"year":"2013","quality_controlled":"1","article_type":"original","oa_version":"None","publication_status":"published","type":"journal_article","author":[{"last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074"},{"full_name":"Ellenbroek, Wouter G.","last_name":"Ellenbroek","first_name":"Wouter G."},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"}],"date_created":"2020-04-30T11:43:42Z","status":"public","_id":"7774","title":"Stability of jammed packings I: The rigidity length scale"},{"publication":"Soft Matter","day":"08","issue":"46","publication_identifier":{"issn":["1744-683X","1744-6848"]},"month":"10","publisher":"Royal Society of Chemistry","article_number":"11000","language":[{"iso":"eng"}],"volume":9,"doi":"10.1039/c3sm51096d","_id":"7775","title":"Stability of jammed packings II: The transverse length scale","author":[{"last_name":"Schoenholz","first_name":"Samuel S.","full_name":"Schoenholz, Samuel S."},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074"},{"full_name":"Kogan, Oleg","last_name":"Kogan","first_name":"Oleg"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"first_name":"Sidney R.","last_name":"Nagel","full_name":"Nagel, Sidney R."}],"date_created":"2020-04-30T11:43:58Z","status":"public","article_type":"original","quality_controlled":"1","year":"2013","type":"journal_article","oa_version":"None","publication_status":"published","abstract":[{"text":"As a function of packing fraction at zero temperature and applied stress, an amorphous packing of spheres exhibits a jamming transition where the system is sensitive to boundary conditions even in the thermodynamic limit. Upon further compression, the system should become insensitive to boundary conditions provided it is sufficiently large. Here we explore the linear response to a large class of boundary perturbations in 2 and 3 dimensions. We consider each finite packing with periodic-boundary conditions as the basis of an infinite square or cubic lattice and study properties of vibrational modes at arbitrary wave vector. We find that the stability of such modes can be understood in terms of a competition between plane waves and the anomalous vibrational modes associated with the jamming transition; infinitesimal boundary perturbations become irrelevant for systems that are larger than a length scale that characterizes the transverse excitations. This previously identified length diverges at the jamming transition.","lang":"eng"}],"intvolume":"         9","extern":"1","date_published":"2013-10-08T00:00:00Z","citation":{"ista":"Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.","ieee":"S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability of jammed packings II: The transverse length scale,” <i>Soft Matter</i>, vol. 9, no. 46. Royal Society of Chemistry, 2013.","short":"S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter 9 (2013).","mla":"Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse Length Scale.” <i>Soft Matter</i>, vol. 9, no. 46, 11000, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3sm51096d\">10.1039/c3sm51096d</a>.","ama":"Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed packings II: The transverse length scale. <i>Soft Matter</i>. 2013;9(46). doi:<a href=\"https://doi.org/10.1039/c3sm51096d\">10.1039/c3sm51096d</a>","apa":"Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., &#38; Nagel, S. R. (2013). Stability of jammed packings II: The transverse length scale. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm51096d\">https://doi.org/10.1039/c3sm51096d</a>","chicago":"Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu, and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm51096d\">https://doi.org/10.1039/c3sm51096d</a>."},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1039/c3sm51096d","date_updated":"2021-01-12T08:15:27Z"},{"volume":78,"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2013.03.022","publisher":"Elsevier","month":"05","publication_identifier":{"issn":["0896-6273"]},"publication":"Neuron","day":"22","issue":"4","date_updated":"2024-01-31T10:15:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1016/j.neuron.2013.03.022","date_published":"2013-05-22T00:00:00Z","citation":{"mla":"Joo, William J., et al. “Linking Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” <i>Neuron</i>, vol. 78, no. 4, Elsevier, 2013, pp. 673–86, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">10.1016/j.neuron.2013.03.022</a>.","ama":"Joo WJ, Sweeney LB, Liang L, Luo L. Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. <i>Neuron</i>. 2013;78(4):673-686. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">10.1016/j.neuron.2013.03.022</a>","short":"W.J. Joo, L.B. Sweeney, L. Liang, L. Luo, Neuron 78 (2013) 673–686.","ieee":"W. J. Joo, L. B. Sweeney, L. Liang, and L. Luo, “Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting,” <i>Neuron</i>, vol. 78, no. 4. Elsevier, pp. 673–686, 2013.","ista":"Joo WJ, Sweeney LB, Liang L, Luo L. 2013. Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. Neuron. 78(4), 673–686.","chicago":"Joo, William J., Lora B. Sweeney, Liang Liang, and Liqun Luo. “Linking Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” <i>Neuron</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">https://doi.org/10.1016/j.neuron.2013.03.022</a>.","apa":"Joo, W. J., Sweeney, L. B., Liang, L., &#38; Luo, L. (2013). Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.03.022\">https://doi.org/10.1016/j.neuron.2013.03.022</a>"},"page":"673-686","article_processing_charge":"No","oa_version":"None","type":"journal_article","publication_status":"published","quality_controlled":"1","article_type":"original","year":"2013","intvolume":"        78","abstract":[{"text":"Neural circuit assembly requires selection of specific cell fates, axonal trajectories, and synaptic targets. By analyzing the function of a secreted semaphorin, Sema-2b, in Drosophila olfactory receptor neuron (ORN) development, we identified multiple molecular and cellular mechanisms that link these events. Notch signaling limits Sema-2b expression to ventromedial ORN classes, within which Sema-2b cell-autonomously sensitizes ORN axons to external semaphorins. Central-brain-derived Sema-2a and Sema-2b attract Sema-2b-expressing axons to the ventromedial trajectory. In addition, Sema-2b/PlexB-mediated axon-axon interactions consolidate this trajectory choice and promote ventromedial axon-bundle formation. Selecting the correct developmental trajectory is ultimately essential for proper target choice. These findings demonstrate that Sema-2b couples ORN axon guidance to postsynaptic target neuron dendrite patterning well before the final target selection phase, and exemplify how a single guidance molecule can drive consecutive stages of neural circuit assembly with the help of sophisticated spatial and temporal regulation.","lang":"eng"}],"extern":"1","title":"Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting","_id":"7785","author":[{"full_name":"Joo, William J.","last_name":"Joo","first_name":"William J."},{"orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger"},{"full_name":"Liang, Liang","first_name":"Liang","last_name":"Liang"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"}],"status":"public","date_created":"2020-04-30T13:19:59Z"},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1662-5110"]},"publication":"Frontiers in Neural Circuits","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:16:38Z","citation":{"mla":"Vogels, Tim P., et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” <i>Frontiers in Neural Circuits</i>, vol. 7, 119, Frontiers Media, 2013, doi:<a href=\"https://doi.org/10.3389/fncir.2013.00119\">10.3389/fncir.2013.00119</a>.","ama":"Vogels TP, Froemke RC, Doyon N, et al. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. <i>Frontiers in Neural Circuits</i>. 2013;7. doi:<a href=\"https://doi.org/10.3389/fncir.2013.00119\">10.3389/fncir.2013.00119</a>","ista":"Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. 2013. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. 7, 119.","ieee":"T. P. Vogels <i>et al.</i>, “Inhibitory synaptic plasticity: Spike timing-dependence and putative network function,” <i>Frontiers in Neural Circuits</i>, vol. 7. Frontiers Media, 2013.","short":"T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei, P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, Frontiers in Neural Circuits 7 (2013).","chicago":"Vogels, Tim P, R. C. Froemke, N. Doyon, M. Gilson, J. S. Haas, R. Liu, A. Maffei, et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” <i>Frontiers in Neural Circuits</i>. Frontiers Media, 2013. <a href=\"https://doi.org/10.3389/fncir.2013.00119\">https://doi.org/10.3389/fncir.2013.00119</a>.","apa":"Vogels, T. P., Froemke, R. C., Doyon, N., Gilson, M., Haas, J. S., Liu, R., … Sprekeler, H. (2013). Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. <i>Frontiers in Neural Circuits</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fncir.2013.00119\">https://doi.org/10.3389/fncir.2013.00119</a>"},"license":"https://creativecommons.org/licenses/by/3.0/","abstract":[{"text":"While the plasticity of excitatory synaptic connections in the brain has been widely studied, the plasticity of inhibitory connections is much less understood. Here, we present recent experimental and theoretical findings concerning the rules of spike timing-dependent inhibitory plasticity and their putative network function. This is a summary of a workshop at the COSYNE conference 2012.","lang":"eng"}],"extern":"1","article_type":"original","type":"journal_article","oa_version":"Published Version","author":[{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P"},{"last_name":"Froemke","first_name":"R. C.","full_name":"Froemke, R. C."},{"full_name":"Doyon, N.","last_name":"Doyon","first_name":"N."},{"first_name":"M.","last_name":"Gilson","full_name":"Gilson, M."},{"full_name":"Haas, J. S.","last_name":"Haas","first_name":"J. S."},{"last_name":"Liu","first_name":"R.","full_name":"Liu, R."},{"first_name":"A.","last_name":"Maffei","full_name":"Maffei, A."},{"first_name":"P.","last_name":"Miller","full_name":"Miller, P."},{"first_name":"C. J.","last_name":"Wierenga","full_name":"Wierenga, C. J."},{"full_name":"Woodin, M. A.","last_name":"Woodin","first_name":"M. A."},{"full_name":"Zenke, F.","last_name":"Zenke","first_name":"F."},{"last_name":"Sprekeler","first_name":"H.","full_name":"Sprekeler, H."}],"status":"public","date_created":"2020-06-25T13:23:50Z","_id":"8030","title":"Inhibitory synaptic plasticity: Spike timing-dependence and putative network function","file":[{"relation":"main_file","creator":"cziletti","access_level":"open_access","checksum":"9c321cb12977d84048712eefa7f0c497","date_created":"2020-07-16T11:23:40Z","success":1,"file_size":1530469,"content_type":"application/pdf","date_updated":"2020-07-16T11:23:40Z","file_name":"2013_FrontNeurCirc_Vogels.pdf","file_id":"8123"}],"doi":"10.3389/fncir.2013.00119","volume":7,"article_number":"119","month":"07","publisher":"Frontiers Media","external_id":{"pmid":["23882186"]},"oa":1,"day":"18","fulldoi":"https://doi.org/10.3389/fncir.2013.00119","article_processing_charge":"No","date_published":"2013-07-18T00:00:00Z","file_date_updated":"2020-07-16T11:23:40Z","has_accepted_license":"1","intvolume":"         7","pmid":1,"year":"2013","quality_controlled":"1","publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"ddc":["570"]}]