[{"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Public Library of Science","intvolume":"         8","date_published":"2013-07-23T00:00:00Z","date_created":"2018-12-11T11:57:51Z","scopus_import":1,"department":[{"_id":"JiFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4432","article_number":"e70050","publication":"PLoS One","date_updated":"2021-01-12T06:57:40Z","year":"2013","oa":1,"has_accepted_license":"1","volume":8,"file":[{"file_id":"4681","date_created":"2018-12-12T10:08:21Z","file_name":"IST-2016-413-v1+1_journal.pone.0070050.pdf","creator":"system","file_size":2294955,"relation":"main_file","date_updated":"2020-07-14T12:45:41Z","access_level":"open_access","content_type":"application/pdf","checksum":"2d47ef47616ef4de1d517d146548184e"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","pubrep_id":"413","citation":{"chicago":"Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070050\">https://doi.org/10.1371/journal.pone.0070050</a>.","mla":"Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” <i>PLoS One</i>, vol. 8, no. 7, e70050, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070050\">10.1371/journal.pone.0070050</a>.","ieee":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová, “Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","apa":"Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., &#38; Zažímalová, E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070050\">https://doi.org/10.1371/journal.pone.0070050</a>","ista":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 8(7), e70050.","ama":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070050\">10.1371/journal.pone.0070050</a>","short":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová, PLoS One 8 (2013)."},"day":"23","file_date_updated":"2020-07-14T12:45:41Z","ddc":["570"],"month":"07","status":"public","publication_status":"published","abstract":[{"text":"Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients.","lang":"eng"}],"issue":"7","doi":"10.1371/journal.pone.0070050","title":"Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells","author":[{"full_name":"Čovanová, Milada","last_name":"Čovanová","first_name":"Milada"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"first_name":"Jan","full_name":"Rychtář, Jan","last_name":"Rychtář"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"}],"_id":"2470"},{"oa_version":"Published Version","month":"07","ddc":["570"],"file_date_updated":"2020-07-14T12:45:41Z","citation":{"chicago":"Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt, Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070013\">https://doi.org/10.1371/journal.pone.0070013</a>.","mla":"Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” <i>PLoS One</i>, vol. 8, no. 7, e70013, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070013\">10.1371/journal.pone.0070013</a>.","ieee":"I. Sanchez-Romero <i>et al.</i>, “Mechanism of protein kinetic stabilization by engineered disulfide crosslinks,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","apa":"Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L., … Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070013\">https://doi.org/10.1371/journal.pone.0070013</a>","ista":"Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L, Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 8(7), e70013.","short":"I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L. Skov, J. Sánchez Ruiz, PLoS One 8 (2013).","ama":"Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070013\">10.1371/journal.pone.0070013</a>"},"pubrep_id":"414","day":"30","volume":8,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-07-14T12:45:41Z","content_type":"application/pdf","checksum":"c0c96cc76ed7ef0d036a31a7e33c9a37","access_level":"open_access","relation":"main_file","file_size":1323666,"creator":"system","file_name":"IST-2016-414-v1+1_journal.pone.0070013.pdf","date_created":"2018-12-12T10:15:07Z","file_id":"5124"}],"doi":"10.1371/journal.pone.0070013","abstract":[{"lang":"eng","text":"The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation."}],"issue":"7","_id":"2471","title":"Mechanism of protein kinetic stabilization by engineered disulfide crosslinks","author":[{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada","full_name":"Sanchez Romero, Inmaculada","last_name":"Sanchez Romero"},{"full_name":"Ariza, Antonio","last_name":"Ariza","first_name":"Antonio"},{"first_name":"Keith","full_name":"Wilson, Keith","last_name":"Wilson"},{"first_name":"Michael","full_name":"Skjøt, Michael","last_name":"Skjøt"},{"last_name":"Vind","full_name":"Vind, Jesper","first_name":"Jesper"},{"first_name":"Leonardo","last_name":"De Maria","full_name":"De Maria, Leonardo"},{"first_name":"Lars","last_name":"Skov","full_name":"Skov, Lars"},{"last_name":"Sánchez Ruiz","full_name":"Sánchez Ruiz, Jose","first_name":"Jose"}],"publication_status":"published","status":"public","date_created":"2018-12-11T11:57:51Z","scopus_import":1,"date_published":"2013-07-30T00:00:00Z","publist_id":"4430","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HaJa"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Public Library of Science","intvolume":"         8","year":"2013","oa":1,"article_number":"e70013","date_updated":"2021-01-12T06:57:41Z","publication":"PLoS One"},{"oa":1,"year":"2013","date_updated":"2021-01-12T06:57:41Z","publication":"PLoS One","article_number":"e70069","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4431","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"date_created":"2018-12-11T11:57:52Z","scopus_import":1,"date_published":"2013-07-29T00:00:00Z","publisher":"Public Library of Science","intvolume":"         8","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","_id":"2472","title":"Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development","author":[{"full_name":"Cazzonelli, Christopher","last_name":"Cazzonelli","first_name":"Christopher"},{"last_name":"Vanstraelen","full_name":"Vanstraelen, Marleen","first_name":"Marleen"},{"orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu"},{"first_name":"Kuide","full_name":"Yin, Kuide","last_name":"Yin"},{"last_name":"Carron Arthur","full_name":"Carron Arthur, Ashley","first_name":"Ashley"},{"first_name":"Nazia","last_name":"Nisar","full_name":"Nisar, Nazia"},{"last_name":"Tarle","full_name":"Tarle, Gauri","first_name":"Gauri"},{"first_name":"Abby","last_name":"Cuttriss","full_name":"Cuttriss, Abby"},{"last_name":"Searle","full_name":"Searle, Iain","first_name":"Iain"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"},{"first_name":"Ulrike","last_name":"Mathesius","full_name":"Mathesius, Ulrike"},{"first_name":"Josette","last_name":"Masle","full_name":"Masle, Josette"},{"full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"full_name":"Pogson, Barry","last_name":"Pogson","first_name":"Barry"}],"doi":"10.1371/journal.pone.0070069","abstract":[{"lang":"eng","text":"Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development."}],"issue":"7","project":[{"call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"},{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"ec_funded":1,"status":"public","publication_status":"published","file_date_updated":"2020-07-14T12:45:41Z","ddc":["580","570"],"month":"07","pubrep_id":"393","citation":{"chicago":"Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070069\">https://doi.org/10.1371/journal.pone.0070069</a>.","mla":"Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” <i>PLoS One</i>, vol. 8, no. 7, e70069, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070069\">10.1371/journal.pone.0070069</a>.","apa":"Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar, N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070069\">https://doi.org/10.1371/journal.pone.0070069</a>","ieee":"C. Cazzonelli <i>et al.</i>, “Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","short":"C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar, G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml, B. Pogson, PLoS One 8 (2013).","ama":"Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070069\">10.1371/journal.pone.0070069</a>","ista":"Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 8(7), e70069."},"day":"29","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-07-14T12:45:41Z","access_level":"open_access","content_type":"application/pdf","checksum":"3be71828b6c2ba9c90eb7056e3f7f57a","file_name":"IST-2015-393-v1+1_journal.pone.0070069.pdf","relation":"main_file","creator":"system","file_size":9003465,"file_id":"5222","date_created":"2018-12-12T10:16:34Z"}],"volume":8,"has_accepted_license":"1"},{"department":[{"_id":"NiBa"}],"publist_id":"4428","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-01-03T00:00:00Z","date_created":"2018-12-11T11:57:52Z","scopus_import":1,"publisher":"Elsevier","intvolume":"        87","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","oa":1,"year":"2013","publication":"Theoretical Population Biology","date_updated":"2021-01-12T06:57:42Z","page":"75 - 89","citation":{"mla":"Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.” <i>Theoretical Population Biology</i>, vol. 87, no. 8, Elsevier, 2013, pp. 75–89, doi:<a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">10.1016/j.tpb.2012.12.001</a>.","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Genetic Hitch-Hiking in Spatially Extended Populations.” <i>Theoretical Population Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">https://doi.org/10.1016/j.tpb.2012.12.001</a>.","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking in spatially extended populations,” <i>Theoretical Population Biology</i>, vol. 87, no. 8. Elsevier, pp. 75–89, 2013.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., &#38; Véber, A. (2013). Genetic hitch-hiking in spatially extended populations. <i>Theoretical Population Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">https://doi.org/10.1016/j.tpb.2012.12.001</a>","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially extended populations. <i>Theoretical Population Biology</i>. 2013;87(8):75-89. doi:<a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">10.1016/j.tpb.2012.12.001</a>","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 87(8), 75–89.","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 75–89."},"pubrep_id":"118","day":"03","month":"01","file_date_updated":"2020-07-14T12:45:41Z","ddc":["570"],"oa_version":"Submitted Version","file":[{"file_id":"5376","date_created":"2018-12-12T10:18:54Z","file_name":"IST-2013-118-v1+1_bartonetalRevision.pdf","relation":"main_file","file_size":1706282,"creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"4274ec1f433b838a7d5b941cc9684ca7","date_updated":"2020-07-14T12:45:41Z"}],"has_accepted_license":"1","volume":87,"title":"Genetic hitch-hiking in spatially extended populations","author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"},{"last_name":"Kelleher","full_name":"Kelleher, Jerome","first_name":"Jerome"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}],"_id":"2473","abstract":[{"text":"When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and  is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift,  . The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement  ; this can be substantial if the species’ range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis.","lang":"eng"}],"issue":"8","doi":"10.1016/j.tpb.2012.12.001","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"status":"public","publication_status":"published","ec_funded":1},{"day":"30","department":[{"_id":"ChLa"}],"citation":{"chicago":"Lampert, Christoph, Hannes Nickisch, and Stefan Harmeling. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2013. <a href=\"https://doi.org/10.1109/TPAMI.2013.140\">https://doi.org/10.1109/TPAMI.2013.140</a>.","mla":"Lampert, Christoph, et al. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 3, IEEE, 2013, pp. 453–65, doi:<a href=\"https://doi.org/10.1109/TPAMI.2013.140\">10.1109/TPAMI.2013.140</a>.","apa":"Lampert, C., Nickisch, H., &#38; Harmeling, S. (2013). Attribute-based classification for zero-shot learning of object categories. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2013.140\">https://doi.org/10.1109/TPAMI.2013.140</a>","ieee":"C. Lampert, H. Nickisch, and S. Harmeling, “Attribute-based classification for zero-shot learning of object categories,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 3. IEEE, pp. 453–465, 2013.","short":"C. Lampert, H. Nickisch, S. Harmeling, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2013) 453–465.","ista":"Lampert C, Nickisch H, Harmeling S. 2013. Attribute-based classification for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis and Machine Intelligence. 36(3), 453–465.","ama":"Lampert C, Nickisch H, Harmeling S. Attribute-based classification for zero-shot learning of object categories. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2013;36(3):453-465. doi:<a href=\"https://doi.org/10.1109/TPAMI.2013.140\">10.1109/TPAMI.2013.140</a>"},"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4385","date_published":"2013-07-30T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:58:08Z","oa_version":"None","intvolume":"        36","publisher":"IEEE","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"volume":36,"author":[{"full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887"},{"last_name":"Nickisch","full_name":"Nickisch, Hannes","first_name":"Hannes"},{"first_name":"Stefan","last_name":"Harmeling","full_name":"Harmeling, Stefan"}],"title":"Attribute-based classification for zero-shot learning of object categories","_id":"2516","issue":"3","year":"2013","abstract":[{"text":"We study the problem of object recognition for categories for which we have no training examples, a task also called zero-data or zero-shot learning. This situation has hardly been studied in computer vision research, even though it occurs frequently: the world contains tens of thousands of different object classes and for only few of them image collections have been formed and suitably annotated. To tackle the problem we introduce attribute-based classification: objects are identified based on a high-level description that is phrased in terms of semantic attributes, such as the object's color or shape. Because the identification of each such property transcends the specific learning task at hand, the attribute classifiers can be pre-learned independently, e.g. from existing image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In this paper we also introduce a new dataset, Animals with Attributes, of over 30,000 images of 50 animal classes, annotated with 85 semantic attributes. Extensive experiments on this and two more datasets show that attribute-based classification indeed is able to categorize images without access to any training images of the target classes.","lang":"eng"}],"doi":"10.1109/TPAMI.2013.140","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","date_updated":"2021-01-12T06:57:58Z","publication_status":"published","status":"public","page":"453 - 465"},{"date_updated":"2020-08-11T10:09:47Z","page":"15 - 27","oa":1,"year":"2013","alternative_title":["LNCS"],"publisher":"Springer","intvolume":"      7966","series_title":"Lecture Notes in Computer Science","type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","publist_id":"4384","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T11:58:08Z","scopus_import":1,"date_published":"2013-07-01T00:00:00Z","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"status":"public","acknowledgement":"ERC Grant QUALITY. ","publication_status":"published","_id":"2517","title":"Formalizing and reasoning about quality","author":[{"full_name":"Almagor, Shaull","last_name":"Almagor","first_name":"Shaull"},{"last_name":"Boker","full_name":"Boker, Udi","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"doi":"10.1007/978-3-642-39212-2_3","abstract":[{"lang":"eng","text":"Traditional formal methods are based on a Boolean satisfaction notion: a reactive system satisfies, or not, a given specification. We generalize formal methods to also address the quality of systems. As an adequate specification formalism we introduce the linear temporal logic LTL[F]. The satisfaction value of an LTL[F] formula is a number between 0 and 1, describing the quality of the satisfaction. The logic generalizes traditional LTL by augmenting it with a (parameterized) set F of arbitrary functions over the interval [0,1]. For example, F may contain the maximum or minimum between the satisfaction values of subformulas, their product, and their average. The classical decision problems in formal methods, such as satisfiability, model checking, and synthesis, are generalized to search and optimization problems in the quantitative setting. For example, model checking asks for the quality in which a specification is satisfied, and synthesis returns a system satisfying the specification with the highest quality. Reasoning about quality gives rise to other natural questions, like the distance between specifications. We formalize these basic questions and study them for LTL[F]. By extending the automata-theoretic approach for LTL to a setting that takes quality into an account, we are able to solve the above problems and show that reasoning about LTL[F] has roughly the same complexity as reasoning about traditional LTL."}],"issue":"Part 2","file":[{"date_created":"2020-05-15T11:16:12Z","file_id":"7860","date_updated":"2020-07-14T12:45:42Z","checksum":"85afbf6c18a2c7e377c52c9410e2d824","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_size":363031,"relation":"main_file","file_name":"2013_ICALP_Almagor.pdf"}],"article_processing_charge":"No","volume":7966,"has_accepted_license":"1","ddc":["000"],"month":"07","file_date_updated":"2020-07-14T12:45:42Z","citation":{"chicago":"Almagor, Shaull, Udi Boker, and Orna Kupferman. “Formalizing and Reasoning about Quality.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">https://doi.org/10.1007/978-3-642-39212-2_3</a>.","mla":"Almagor, Shaull, et al. <i>Formalizing and Reasoning about Quality</i>. Vol. 7966, no. Part 2, Springer, 2013, pp. 15–27, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">10.1007/978-3-642-39212-2_3</a>.","short":"S. Almagor, U. Boker, O. Kupferman, 7966 (2013) 15–27.","ista":"Almagor S, Boker U, Kupferman O. 2013. Formalizing and reasoning about quality. 7966(Part 2), 15–27.","ama":"Almagor S, Boker U, Kupferman O. Formalizing and reasoning about quality. 2013;7966(Part 2):15-27. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">10.1007/978-3-642-39212-2_3</a>","ieee":"S. Almagor, U. Boker, and O. Kupferman, “Formalizing and reasoning about quality,” vol. 7966, no. Part 2. Springer, pp. 15–27, 2013.","apa":"Almagor, S., Boker, U., &#38; Kupferman, O. (2013). Formalizing and reasoning about quality. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">https://doi.org/10.1007/978-3-642-39212-2_3</a>"},"day":"01","oa_version":"Submitted Version","conference":{"name":"ICALP: Automata, Languages and Programming","end_date":"2013-07-12","location":"Riga, Latvia","start_date":"2013-07-08"}},{"publisher":"Springer","main_file_link":[{"url":"http://arxiv.org/abs/1207.7213","open_access":"1"}],"intvolume":"      7965","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"VlKo"}],"publist_id":"4383","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2013-07-01T00:00:00Z","external_id":{"arxiv":["1207.7213"]},"date_created":"2018-12-11T11:58:08Z","scopus_import":1,"date_updated":"2023-02-23T10:35:42Z","related_material":{"record":[{"id":"2271","status":"public","relation":"later_version"}]},"page":"625 - 636","oa":1,"year":"2013","alternative_title":["LNCS"],"arxiv":1,"volume":7965,"citation":{"chicago":"Kolmogorov, Vladimir. “The Power of Linear Programming for Finite-Valued CSPs: A Constructive Characterization,” 7965:625–36. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">https://doi.org/10.1007/978-3-642-39206-1_53</a>.","mla":"Kolmogorov, Vladimir. <i>The Power of Linear Programming for Finite-Valued CSPs: A Constructive Characterization</i>. Vol. 7965, no. 1, Springer, 2013, pp. 625–36, doi:<a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">10.1007/978-3-642-39206-1_53</a>.","ama":"Kolmogorov V. The power of linear programming for finite-valued CSPs: A constructive characterization. In: Vol 7965. Springer; 2013:625-636. doi:<a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">10.1007/978-3-642-39206-1_53</a>","short":"V. Kolmogorov, in:, Springer, 2013, pp. 625–636.","ista":"Kolmogorov V. 2013. The power of linear programming for finite-valued CSPs: A constructive characterization. ICALP: Automata, Languages and Programming, LNCS, vol. 7965, 625–636.","apa":"Kolmogorov, V. (2013). The power of linear programming for finite-valued CSPs: A constructive characterization (Vol. 7965, pp. 625–636). Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">https://doi.org/10.1007/978-3-642-39206-1_53</a>","ieee":"V. Kolmogorov, “The power of linear programming for finite-valued CSPs: A constructive characterization,” presented at the ICALP: Automata, Languages and Programming, Riga, Latvia, 2013, vol. 7965, no. 1, pp. 625–636."},"day":"01","month":"07","oa_version":"Preprint","conference":{"location":"Riga, Latvia","start_date":"2013-07-08","end_date":"2013-07-12","name":"ICALP: Automata, Languages and Programming"},"publication_status":"published","status":"public","title":"The power of linear programming for finite-valued CSPs: A constructive characterization","author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"}],"_id":"2518","abstract":[{"text":"A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. An instance of the problem is specified by a sum of cost functions from the language with the goal to minimise the sum. We study which classes of finite-valued languages can be solved exactly by the basic linear programming relaxation (BLP). Thapper and Živný showed [20] that if BLP solves the language then the language admits a binary commutative fractional polymorphism. We prove that the converse is also true. This leads to a necessary and a sufficient condition which can be checked in polynomial time for a given language. In contrast, the previous necessary and sufficient condition due to [20] involved infinitely many inequalities. More recently, Thapper and Živný [21] showed (using, in particular, a technique introduced in this paper) that core languages that do not satisfy our condition are NP-hard. Taken together, these results imply that a finite-valued language can either be solved using Linear Programming or is NP-hard.","lang":"eng"}],"issue":"1","doi":"10.1007/978-3-642-39206-1_53"},{"publication_identifier":{"isbn":["9780974903996"]},"status":"public","publication_status":"published","title":"The supervised IBP: Neighbourhood preserving infinite latent feature models","author":[{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia","last_name":"Sharmanska","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia"},{"last_name":"Knowles","full_name":"Knowles, David","first_name":"David"},{"first_name":"Zoubin","last_name":"Ghahramani","full_name":"Ghahramani, Zoubin"}],"_id":"2520","abstract":[{"lang":"eng","text":"We propose a probabilistic model to infer supervised latent variables in\r\nthe Hamming space from observed data. Our model allows simultaneous\r\ninference of the number of binary latent variables, and their values. The\r\nlatent variables preserve neighbourhood structure of the data in a sense\r\nthat objects in the same semantic concept have similar latent values, and\r\nobjects in different concepts have dissimilar latent values. We formulate\r\nthe supervised infinite latent variable problem based on an intuitive\r\nprinciple of pulling objects together if they are of the same type, and\r\npushing them apart if they are not. We then combine this principle with a\r\nflexible Indian Buffet Process prior on the latent variables. We show that\r\nthe inferred supervised latent variables can be directly used to perform a\r\nnearest neighbour search for the purpose of retrieval.  We introduce a new\r\napplication of dynamically extending hash codes, and show how to\r\neffectively couple the structure of the hash codes with continuously\r\ngrowing structure of the neighbourhood preserving infinite latent feature\r\nspace."}],"file":[{"file_name":"IST-2013-137-v1+1_QuaShaKnoGha13.pdf","relation":"main_file","file_size":1117100,"creator":"system","date_updated":"2020-07-14T12:45:42Z","access_level":"open_access","content_type":"application/pdf","checksum":"325f20c4b926bd74d39006b97df572bd","file_id":"5134","date_created":"2018-12-12T10:15:16Z"}],"has_accepted_license":"1","pubrep_id":"137","citation":{"apa":"Quadrianto, N., Sharmanska, V., Knowles, D., &#38; Ghahramani, Z. (2013). The supervised IBP: Neighbourhood preserving infinite latent feature models. In <i>Proceedings of the 29th conference uncertainty in Artificial Intelligence</i> (pp. 527–536). Bellevue, WA, United States: AUAI Press.","ieee":"N. Quadrianto, V. Sharmanska, D. Knowles, and Z. Ghahramani, “The supervised IBP: Neighbourhood preserving infinite latent feature models,” in <i>Proceedings of the 29th conference uncertainty in Artificial Intelligence</i>, Bellevue, WA, United States, 2013, pp. 527–536.","ama":"Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. The supervised IBP: Neighbourhood preserving infinite latent feature models. In: <i>Proceedings of the 29th Conference Uncertainty in Artificial Intelligence</i>. AUAI Press; 2013:527-536.","ista":"Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. 2013. The supervised IBP: Neighbourhood preserving infinite latent feature models. Proceedings of the 29th conference uncertainty in Artificial Intelligence. UAI: Uncertainty in Artificial Intelligence, 527–536.","short":"N. Quadrianto, V. Sharmanska, D. Knowles, Z. Ghahramani, in:, Proceedings of the 29th Conference Uncertainty in Artificial Intelligence, AUAI Press, 2013, pp. 527–536.","chicago":"Quadrianto, Novi, Viktoriia Sharmanska, David Knowles, and Zoubin Ghahramani. “The Supervised IBP: Neighbourhood Preserving Infinite Latent Feature Models.” In <i>Proceedings of the 29th Conference Uncertainty in Artificial Intelligence</i>, 527–36. AUAI Press, 2013.","mla":"Quadrianto, Novi, et al. “The Supervised IBP: Neighbourhood Preserving Infinite Latent Feature Models.” <i>Proceedings of the 29th Conference Uncertainty in Artificial Intelligence</i>, AUAI Press, 2013, pp. 527–36."},"day":"11","month":"07","ddc":["000"],"file_date_updated":"2020-07-14T12:45:42Z","oa_version":"Submitted Version","conference":{"name":"UAI: Uncertainty in Artificial Intelligence","location":"Bellevue, WA, United States","start_date":"2013-07-11","end_date":"2013-07-15"},"publication":"Proceedings of the 29th conference uncertainty in Artificial Intelligence","date_updated":"2023-02-23T10:46:36Z","page":"527 - 536","oa":1,"year":"2013","publisher":"AUAI Press","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"ChLa"}],"publist_id":"4381","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-07-11T00:00:00Z","date_created":"2018-12-11T11:58:09Z","scopus_import":1},{"oa_version":"Preprint","day":"16","citation":{"short":"L. Erdös, S. Fournais, J. Solovej, Journal of the European Mathematical Society 15 (2013) 2093–2113.","ama":"Erdös L, Fournais S, Solovej J. Stability and semiclassics in self-generated fields. <i>Journal of the European Mathematical Society</i>. 2013;15(6):2093-2113. doi:<a href=\"https://doi.org/10.4171/JEMS/416\">10.4171/JEMS/416</a>","ista":"Erdös L, Fournais S, Solovej J. 2013. Stability and semiclassics in self-generated fields. Journal of the European Mathematical Society. 15(6), 2093–2113.","apa":"Erdös, L., Fournais, S., &#38; Solovej, J. (2013). Stability and semiclassics in self-generated fields. <i>Journal of the European Mathematical Society</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/JEMS/416\">https://doi.org/10.4171/JEMS/416</a>","ieee":"L. Erdös, S. Fournais, and J. Solovej, “Stability and semiclassics in self-generated fields,” <i>Journal of the European Mathematical Society</i>, vol. 15, no. 6. European Mathematical Society, pp. 2093–2113, 2013.","mla":"Erdös, László, et al. “Stability and Semiclassics in Self-Generated Fields.” <i>Journal of the European Mathematical Society</i>, vol. 15, no. 6, European Mathematical Society, 2013, pp. 2093–113, doi:<a href=\"https://doi.org/10.4171/JEMS/416\">10.4171/JEMS/416</a>.","chicago":"Erdös, László, Søren Fournais, and Jan Solovej. “Stability and Semiclassics in Self-Generated Fields.” <i>Journal of the European Mathematical Society</i>. European Mathematical Society, 2013. <a href=\"https://doi.org/10.4171/JEMS/416\">https://doi.org/10.4171/JEMS/416</a>."},"month":"10","volume":15,"arxiv":1,"issue":"6","abstract":[{"lang":"eng","text":"We consider non-interacting particles subject to a fixed external potential V and a self-generated magnetic field B. The total energy includes the field energy β∫B2 and we minimize over all particle states and magnetic fields. In the case of spin-1/2 particles this minimization leads to the coupled Maxwell-Pauli system. The parameter β tunes the coupling strength between the field and the particles and it effectively determines the strength of the field. We investigate the stability and the semiclassical asymptotics, h→0, of the total ground state energy E(β,h,V). The relevant parameter measuring the field strength in the semiclassical limit is κ=βh. We are not able to give the exact leading order semiclassical asymptotics uniformly in κ or even for fixed κ. We do however give upper and lower bounds on E with almost matching dependence on κ. In the simultaneous limit h→0 and κ→∞ we show that the standard non-magnetic Weyl asymptotics holds. The same result also holds for the spinless case, i.e. where the Pauli operator is replaced by the Schrödinger operator."}],"doi":"10.4171/JEMS/416","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"first_name":"Søren","last_name":"Fournais","full_name":"Fournais, Søren"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"title":"Stability and semiclassics in self-generated fields","_id":"2698","status":"public","publication_status":"published","date_published":"2013-10-16T00:00:00Z","external_id":{"arxiv":["1105.0506"]},"date_created":"2018-12-11T11:59:07Z","department":[{"_id":"LaEr"}],"publist_id":"4198","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"        15","main_file_link":[{"url":"http://arxiv.org/abs/1105.0506","open_access":"1"}],"publisher":"European Mathematical Society","year":"2013","oa":1,"page":"2093 - 2113","publication":"Journal of the European Mathematical Society","date_updated":"2021-01-12T06:59:07Z"},{"date_updated":"2021-01-12T06:59:15Z","publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","page":"1573 - 1580","oa":1,"year":"2013","publisher":"ACM","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4174","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"date_created":"2018-12-11T11:59:14Z","scopus_import":1,"date_published":"2013-07-01T00:00:00Z","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publication_status":"published","status":"public","_id":"2718","title":"Can quantitative and population genetics help us understand evolutionary computation?","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"Paixao, Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","orcid":"0000-0003-2361-3953"}],"doi":"10.1145/2463372.2463568","abstract":[{"lang":"eng","text":"Even though both population and quantitative genetics, and evolutionary computation, deal with the same questions, they have developed largely independently of each other. I review key results from each field, emphasising those that apply independently of the (usually unknown) relation between genotype and phenotype. The infinitesimal model provides a simple framework for predicting the response of complex traits to selection, which in biology has proved remarkably successful. This allows one to choose the schedule of population sizes and selection intensities that will maximise the response to selection, given that the total number of individuals realised, C = ∑t Nt, is constrained. This argument shows that for an additive trait (i.e., determined by the sum of effects of the genes), the optimum population size and the maximum possible response (i.e., the total change in trait mean) are both proportional to √C."}],"file":[{"file_id":"5159","date_created":"2018-12-12T10:15:38Z","access_level":"open_access","content_type":"application/pdf","checksum":"9d9be9090ce5c20766e0eb076ace5b98","date_updated":"2020-07-14T12:45:45Z","file_name":"IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf","relation":"main_file","file_size":475844,"creator":"system"}],"has_accepted_license":"1","ddc":["570"],"file_date_updated":"2020-07-14T12:45:45Z","month":"07","pubrep_id":"564","citation":{"chicago":"Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” In <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, 1573–80. ACM, 2013. <a href=\"https://doi.org/10.1145/2463372.2463568\">https://doi.org/10.1145/2463372.2463568</a>.","mla":"Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2013, pp. 1573–80, doi:<a href=\"https://doi.org/10.1145/2463372.2463568\">10.1145/2463372.2463568</a>.","ieee":"N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i>, Amsterdam, Netherlands, 2013, pp. 1573–1580.","apa":"Barton, N. H., &#38; Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i> (pp. 1573–1580). Amsterdam, Netherlands: ACM. <a href=\"https://doi.org/10.1145/2463372.2463568\">https://doi.org/10.1145/2463372.2463568</a>","ista":"Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580.","ama":"Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2013:1573-1580. doi:<a href=\"https://doi.org/10.1145/2463372.2463568\">10.1145/2463372.2463568</a>","short":"N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580."},"day":"01","oa_version":"Submitted Version","conference":{"name":"GECCO: Genetic and evolutionary computation conference","start_date":"2013-07-06","location":"Amsterdam, Netherlands","end_date":"2013-07-10"}},{"publisher":"ACM","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"citation":{"ama":"Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2013:845-852. doi:<a href=\"https://doi.org/10.1145/2463372.2463470\">10.1145/2463372.2463470</a>","short":"T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.","ista":"Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852.","ieee":"T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i>, Amsterdam, Netherlands, 2013, pp. 845–852.","apa":"Paixao, T., &#38; Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i> (pp. 845–852). Amsterdam, Netherlands: ACM. <a href=\"https://doi.org/10.1145/2463372.2463470\">https://doi.org/10.1145/2463372.2463470</a>","mla":"Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2013, pp. 845–52, doi:<a href=\"https://doi.org/10.1145/2463372.2463470\">10.1145/2463372.2463470</a>.","chicago":"Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, 845–52. ACM, 2013. <a href=\"https://doi.org/10.1145/2463372.2463470\">https://doi.org/10.1145/2463372.2463470</a>."},"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"day":"01","month":"07","publist_id":"4173","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-07-01T00:00:00Z","date_created":"2018-12-11T11:59:15Z","oa_version":"None","scopus_import":1,"conference":{"name":"GECCO: Genetic and evolutionary computation conference","start_date":"2013-07-06","location":"Amsterdam, Netherlands","end_date":"2013-07-10"},"publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"date_updated":"2021-01-12T06:59:15Z","publication_status":"published","status":"public","page":"845 - 852","ec_funded":1,"title":"A variance decomposition approach to the analysis of genetic algorithms","author":[{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Paixao, Tiago","last_name":"Paixao"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"_id":"2719","abstract":[{"text":"Prediction of the evolutionary process is a long standing problem both in the theory of evolutionary biology and evolutionary computation (EC). It has long been realized that heritable variation is crucial to both the response to selection and the success of genetic algorithms. However, not all variation contributes in the same way to the response. Quantitative genetics has developed a large body of work trying to estimate and understand how different components of the variance in fitness in the population contribute to the response to selection. We illustrate how to apply some concepts of quantitative genetics to the analysis of genetic algorithms. In particular, we derive estimates for the short term prediction of the response to selection and we use variance decomposition to gain insight on local aspects of the landscape. Finally, we propose a new population based genetic algorithm that uses these methods to improve its operation.","lang":"eng"}],"year":"2013","doi":"10.1145/2463372.2463470"},{"_id":"2720","title":"Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila","author":[{"full_name":"Long, Hongan","last_name":"Long","first_name":"Hongan"},{"full_name":"Paixao, Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","orcid":"0000-0003-2361-3953"},{"last_name":"Azevedo","full_name":"Azevedo, Ricardo","first_name":"Ricardo"},{"full_name":"Zufall, Rebecca","last_name":"Zufall","first_name":"Rebecca"}],"doi":"10.1534/genetics.113.153536","abstract":[{"text":"Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is &lt;10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.","lang":"eng"}],"issue":"2","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"status":"public","publication_status":"published","month":"10","pmid":1,"citation":{"chicago":"Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” <i>Genetics</i>. Genetics Society of America, 2013. <a href=\"https://doi.org/10.1534/genetics.113.153536\">https://doi.org/10.1534/genetics.113.153536</a>.","mla":"Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” <i>Genetics</i>, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:<a href=\"https://doi.org/10.1534/genetics.113.153536\">10.1534/genetics.113.153536</a>.","ista":"Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.","short":"H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.","ama":"Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. <i>Genetics</i>. 2013;195(2):527-540. doi:<a href=\"https://doi.org/10.1534/genetics.113.153536\">10.1534/genetics.113.153536</a>","apa":"Long, H., Paixao, T., Azevedo, R., &#38; Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.113.153536\">https://doi.org/10.1534/genetics.113.153536</a>","ieee":"H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” <i>Genetics</i>, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013."},"day":"01","oa_version":"Submitted Version","volume":195,"article_processing_charge":"No","oa":1,"year":"2013","date_updated":"2021-01-12T06:59:16Z","publication":"Genetics","page":"527-540","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"4172","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"date_created":"2018-12-11T11:59:15Z","scopus_import":1,"external_id":{"pmid":["23934880"]},"date_published":"2013-10-01T00:00:00Z","publisher":"Genetics Society of America","intvolume":"       195","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/","open_access":"1"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article"},{"publication_status":"published","status":"public","title":"Local eigenvalue density for general MANOVA matrices","author":[{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"first_name":"Brendan","last_name":"Farrell","full_name":"Farrell, Brendan"}],"_id":"2782","abstract":[{"text":"We consider random n×n matrices of the form (XX*+YY*)^{-1/2}YY*(XX*+YY*)^{-1/2}, where X and Y have independent entries with zero mean and variance one. These matrices are the natural generalization of the Gaussian case, which are known as MANOVA matrices and which have joint eigenvalue density given by the third classical ensemble, the Jacobi ensemble. We show that, away from the spectral edge, the eigenvalue density converges to the limiting density of the Jacobi ensemble even on the shortest possible scales of order 1/n (up to log n factors). This result is the analogue of the local Wigner semicircle law and the local Marchenko-Pastur law for general MANOVA matrices.","lang":"eng"}],"issue":"6","doi":"10.1007/s10955-013-0807-8","arxiv":1,"volume":152,"citation":{"apa":"Erdös, L., &#38; Farrell, B. (2013). Local eigenvalue density for general MANOVA matrices. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s10955-013-0807-8\">https://doi.org/10.1007/s10955-013-0807-8</a>","ieee":"L. Erdös and B. Farrell, “Local eigenvalue density for general MANOVA matrices,” <i>Journal of Statistical Physics</i>, vol. 152, no. 6. Springer, pp. 1003–1032, 2013.","ama":"Erdös L, Farrell B. Local eigenvalue density for general MANOVA matrices. <i>Journal of Statistical Physics</i>. 2013;152(6):1003-1032. doi:<a href=\"https://doi.org/10.1007/s10955-013-0807-8\">10.1007/s10955-013-0807-8</a>","short":"L. Erdös, B. Farrell, Journal of Statistical Physics 152 (2013) 1003–1032.","ista":"Erdös L, Farrell B. 2013. Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. 152(6), 1003–1032.","chicago":"Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” <i>Journal of Statistical Physics</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s10955-013-0807-8\">https://doi.org/10.1007/s10955-013-0807-8</a>.","mla":"Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” <i>Journal of Statistical Physics</i>, vol. 152, no. 6, Springer, 2013, pp. 1003–32, doi:<a href=\"https://doi.org/10.1007/s10955-013-0807-8\">10.1007/s10955-013-0807-8</a>."},"day":"18","month":"07","oa_version":"Preprint","publication":"Journal of Statistical Physics","date_updated":"2021-01-12T06:59:41Z","page":"1003 - 1032","oa":1,"year":"2013","publisher":"Springer","intvolume":"       152","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.0031"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"LaEr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4107","external_id":{"arxiv":["1207.0031"]},"date_published":"2013-07-18T00:00:00Z","date_created":"2018-12-11T11:59:34Z","scopus_import":1},{"publication":"Review of Scientific Instruments","date_updated":"2021-01-12T06:59:50Z","status":"public","publication_status":"published","article_number":"065106","title":"High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects","author":[{"first_name":"Kerstin","full_name":"Avila, Kerstin","last_name":"Avila"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"_id":"2806","abstract":[{"text":"A novel Taylor-Couette system has been constructed for investigations of transitional as well as high Reynolds number turbulent flows in very large aspect ratios. The flexibility of the setup enables studies of a variety of problems regarding hydrodynamic instabilities and turbulence in rotating flows. The inner and outer cylinders and the top and bottom endplates can be rotated independently with rotation rates of up to 30 Hz, thereby covering five orders of magnitude in Reynolds numbers (Re = 101-106). The radius ratio can be easily changed, the highest realized one is η = 0.98 corresponding to an aspect ratio of 260 gap width in the vertical and 300 in the azimuthal direction. For η &lt; 0.98 the aspect ratio can be dynamically changed during measurements and complete transparency in the radial direction over the full length of the cylinders is provided by the usage of a precision glass inner cylinder. The temperatures of both cylinders are controlled independently. Overall this apparatus combines an unmatched variety in geometry, rotation rates, and temperatures, which is provided by a sophisticated high-precision bearing system. Possible applications are accurate studies of the onset of turbulence and spatio-temporal intermittent flow patterns in very large domains, transport processes of turbulence at high Re, the stability of Keplerian flows for different boundary conditions, and studies of baroclinic instabilities.","lang":"eng"}],"year":"2013","issue":"6","doi":"10.1063/1.4807704","publisher":"American Institute of Physics","intvolume":"        84","volume":84,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"citation":{"chicago":"Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” <i>Review of Scientific Instruments</i>. American Institute of Physics, 2013. <a href=\"https://doi.org/10.1063/1.4807704\">https://doi.org/10.1063/1.4807704</a>.","mla":"Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” <i>Review of Scientific Instruments</i>, vol. 84, no. 6, 065106, American Institute of Physics, 2013, doi:<a href=\"https://doi.org/10.1063/1.4807704\">10.1063/1.4807704</a>.","apa":"Avila, K., &#38; Hof, B. (2013). High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. <i>Review of Scientific Instruments</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4807704\">https://doi.org/10.1063/1.4807704</a>","ieee":"K. Avila and B. Hof, “High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects,” <i>Review of Scientific Instruments</i>, vol. 84, no. 6. American Institute of Physics, 2013.","ama":"Avila K, Hof B. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. <i>Review of Scientific Instruments</i>. 2013;84(6). doi:<a href=\"https://doi.org/10.1063/1.4807704\">10.1063/1.4807704</a>","short":"K. Avila, B. Hof, Review of Scientific Instruments 84 (2013).","ista":"Avila K, Hof B. 2013. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. 84(6), 065106."},"department":[{"_id":"BjHo"}],"day":"06","publist_id":"4081","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","date_published":"2013-06-06T00:00:00Z","date_created":"2018-12-11T11:59:42Z","oa_version":"None","scopus_import":1},{"page":"595 - 604","publication":"45th Annual ACM Symposium on theory of computing","date_updated":"2021-01-12T06:59:51Z","year":"2013","oa":1,"type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"ACM","date_published":"2013-06-01T00:00:00Z","date_created":"2018-12-11T11:59:42Z","scopus_import":1,"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4078","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"We consider several basic problems of algebraic topology, with connections to combinatorial and geometric questions, from the point of view of computational complexity. The extension problem asks, given topological spaces X; Y , a subspace A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X → Y . For computational purposes, we assume that X and Y are represented as finite simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map. In this generality the problem is undecidable, as follows from Novikov's result from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected; informally, this means that Y has \\no holes up to dimension k-1&quot; (a basic example of such a Y is the sphere Sk). We prove that, on the one hand, this problem is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2, we obtain an algorithm that solves the extension problem in polynomial time assuming Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides a classification of all extensions up to homotopy (continuous deformation). This relies on results of our SODA 2012 paper, and the main new ingredient is a machinery of objects with polynomial-time homology, which is a polynomial-time analog of objects with effective homology developed earlier by Sergeraert et al. We also consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected Y . Their computability was established by Brown in 1957; we show that πk(Y ) can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where Y is a cell complex with certain rather compact encoding. We strengthen his result to #P-hardness for Y given as a simplicial complex. "}],"doi":"10.1145/2488608.2488683","title":"Extending continuous maps: Polynomiality and undecidability","author":[{"full_name":"Čadek, Martin","last_name":"Čadek","first_name":"Martin"},{"last_name":"Krcál","full_name":"Krcál, Marek","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiří","full_name":"Matoušek, Jiří","last_name":"Matoušek"},{"full_name":"Vokřínek, Lukáš","last_name":"Vokřínek","first_name":"Lukáš"},{"orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Uli"}],"_id":"2807","has_accepted_license":"1","file":[{"file_id":"5081","date_created":"2018-12-12T10:14:29Z","access_level":"open_access","checksum":"06c2ce5c1135fbc1f71ca15eeb242dcf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:48Z","file_name":"IST-2016-533-v1+1_Extending_continuous_maps_polynomiality_and_undecidability.pdf","relation":"main_file","file_size":447945,"creator":"system"}],"oa_version":"Submitted Version","conference":{"start_date":"2013-06-01","location":"Palo Alto, CA, United States","end_date":"2013-06-04","name":"STOC: Symposium on the Theory of Computing"},"pubrep_id":"533","citation":{"ieee":"M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, and U. Wagner, “Extending continuous maps: Polynomiality and undecidability,” in <i>45th Annual ACM Symposium on theory of computing</i>, Palo Alto, CA, United States, 2013, pp. 595–604.","apa":"Čadek, M., Krcál, M., Matoušek, J., Vokřínek, L., &#38; Wagner, U. (2013). Extending continuous maps: Polynomiality and undecidability. In <i>45th Annual ACM Symposium on theory of computing</i> (pp. 595–604). Palo Alto, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2488608.2488683\">https://doi.org/10.1145/2488608.2488683</a>","ama":"Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. Extending continuous maps: Polynomiality and undecidability. In: <i>45th Annual ACM Symposium on Theory of Computing</i>. ACM; 2013:595-604. doi:<a href=\"https://doi.org/10.1145/2488608.2488683\">10.1145/2488608.2488683</a>","short":"M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, U. Wagner, in:, 45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604.","ista":"Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. 2013. Extending continuous maps: Polynomiality and undecidability. 45th Annual ACM Symposium on theory of computing. STOC: Symposium on the Theory of Computing, 595–604.","chicago":"Čadek, Martin, Marek Krcál, Jiří Matoušek, Lukáš Vokřínek, and Uli Wagner. “Extending Continuous Maps: Polynomiality and Undecidability.” In <i>45th Annual ACM Symposium on Theory of Computing</i>, 595–604. ACM, 2013. <a href=\"https://doi.org/10.1145/2488608.2488683\">https://doi.org/10.1145/2488608.2488683</a>.","mla":"Čadek, Martin, et al. “Extending Continuous Maps: Polynomiality and Undecidability.” <i>45th Annual ACM Symposium on Theory of Computing</i>, ACM, 2013, pp. 595–604, doi:<a href=\"https://doi.org/10.1145/2488608.2488683\">10.1145/2488608.2488683</a>."},"day":"01","file_date_updated":"2020-07-14T12:45:48Z","ddc":["510"],"month":"06"},{"day":"03","citation":{"mla":"Landberg, Katarina, et al. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” <i>Plant Physiology</i>, vol. 162, no. 3, American Society of Plant Biologists, 2013, pp. 1406–19, doi:<a href=\"https://doi.org/10.1104/pp.113.214023\">10.1104/pp.113.214023</a>.","chicago":"Landberg, Katarina, Eric Pederson, Tom Viaene, Behruz Bozorg, Jiří Friml, Henrik Jönsson, Mattias Thelander, and Eva Sundberg. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1104/pp.113.214023\">https://doi.org/10.1104/pp.113.214023</a>.","short":"K. Landberg, E. Pederson, T. Viaene, B. Bozorg, J. Friml, H. Jönsson, M. Thelander, E. Sundberg, Plant Physiology 162 (2013) 1406–1419.","ama":"Landberg K, Pederson E, Viaene T, et al. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. <i>Plant Physiology</i>. 2013;162(3):1406-1419. doi:<a href=\"https://doi.org/10.1104/pp.113.214023\">10.1104/pp.113.214023</a>","ista":"Landberg K, Pederson E, Viaene T, Bozorg B, Friml J, Jönsson H, Thelander M, Sundberg E. 2013. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. 162(3), 1406–1419.","apa":"Landberg, K., Pederson, E., Viaene, T., Bozorg, B., Friml, J., Jönsson, H., … Sundberg, E. (2013). The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.113.214023\">https://doi.org/10.1104/pp.113.214023</a>","ieee":"K. Landberg <i>et al.</i>, “The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain,” <i>Plant Physiology</i>, vol. 162, no. 3. American Society of Plant Biologists, pp. 1406–1419, 2013."},"month":"07","pmid":1,"oa_version":"Submitted Version","volume":162,"author":[{"last_name":"Landberg","full_name":"Landberg, Katarina","first_name":"Katarina"},{"last_name":"Pederson","full_name":"Pederson, Eric","first_name":"Eric"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"full_name":"Bozorg, Behruz","last_name":"Bozorg","first_name":"Behruz"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí"},{"full_name":"Jönsson, Henrik","last_name":"Jönsson","first_name":"Henrik"},{"first_name":"Mattias","last_name":"Thelander","full_name":"Thelander, Mattias"},{"last_name":"Sundberg","full_name":"Sundberg, Eva","first_name":"Eva"}],"title":"The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain","_id":"2808","issue":"3","abstract":[{"text":"In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/ STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3pro:GUS and PpPINApro:GFP-GUS, and the auxin-conjugating transgene PpSHI2pro:IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs.","lang":"eng"}],"doi":"10.1104/pp.113.214023","status":"public","publication_status":"published","department":[{"_id":"JiFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4079","date_published":"2013-07-03T00:00:00Z","external_id":{"pmid":["23669745"]},"scopus_import":1,"date_created":"2018-12-11T11:59:42Z","intvolume":"       162","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707547/","open_access":"1"}],"publisher":"American Society of Plant Biologists","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","oa":1,"year":"2013","publication":"Plant Physiology","date_updated":"2021-01-12T06:59:51Z","page":"1406 - 1419"},{"publisher":"Public Library of Science","intvolume":"         9","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publist_id":"4075","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToBo"}],"date_created":"2018-12-11T11:59:43Z","scopus_import":1,"date_published":"2013-06-27T00:00:00Z","date_updated":"2021-01-12T06:59:52Z","publication":"PLoS Genetics","article_number":"e1003580","oa":1,"year":"2013","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","creator":"system","file_size":474655,"file_name":"IST-2016-412-v1+1_journal.pgen.1003580.pdf","date_updated":"2020-07-14T12:45:48Z","content_type":"application/pdf","checksum":"7a4736dd80496d29ff6908b6f2329b4e","access_level":"open_access","date_created":"2018-12-12T10:08:51Z","file_id":"4713"}],"volume":9,"has_accepted_license":"1","month":"06","file_date_updated":"2020-07-14T12:45:48Z","ddc":["570"],"pubrep_id":"412","citation":{"ieee":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, and S. Tans, “Environmental dependence of genetic constraint,” <i>PLoS Genetics</i>, vol. 9, no. 6. Public Library of Science, 2013.","apa":"de Vos, M., Poelwijk, F., Battich, N., Ndika, J., &#38; Tans, S. (2013). Environmental dependence of genetic constraint. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1003580\">https://doi.org/10.1371/journal.pgen.1003580</a>","ama":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. Environmental dependence of genetic constraint. <i>PLoS Genetics</i>. 2013;9(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003580\">10.1371/journal.pgen.1003580</a>","ista":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. 2013. Environmental dependence of genetic constraint. PLoS Genetics. 9(6), e1003580.","short":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, S. Tans, PLoS Genetics 9 (2013).","mla":"de Vos, Marjon, et al. “Environmental Dependence of Genetic Constraint.” <i>PLoS Genetics</i>, vol. 9, no. 6, e1003580, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003580\">10.1371/journal.pgen.1003580</a>.","chicago":"Vos, Marjon de, Frank Poelwijk, Nico Battich, Joseph Ndika, and Sander Tans. “Environmental Dependence of Genetic Constraint.” <i>PLoS Genetics</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pgen.1003580\">https://doi.org/10.1371/journal.pgen.1003580</a>."},"day":"27","oa_version":"Published Version","status":"public","publication_status":"published","_id":"2810","title":"Environmental dependence of genetic constraint","author":[{"id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","first_name":"Marjon","full_name":"De Vos, Marjon","last_name":"De Vos"},{"first_name":"Frank","full_name":"Poelwijk, Frank","last_name":"Poelwijk"},{"first_name":"Nico","full_name":"Battich, Nico","last_name":"Battich"},{"first_name":"Joseph","full_name":"Ndika, Joseph","last_name":"Ndika"},{"last_name":"Tans","full_name":"Tans, Sander","first_name":"Sander"}],"doi":"10.1371/journal.pgen.1003580","abstract":[{"text":"The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data.","lang":"eng"}],"issue":"6"},{"article_number":"063012","date_updated":"2021-01-12T06:59:53Z","publication":"Physical Review E","year":"2013","oa":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1306.5890"}],"intvolume":"        87","publisher":"American Institute of Physics","scopus_import":1,"date_created":"2018-12-11T11:59:43Z","external_id":{"arxiv":["1306.5890"]},"date_published":"2013-06-18T00:00:00Z","publist_id":"4074","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BjHo"}],"ec_funded":1,"status":"public","publication_status":"published","project":[{"call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589"}],"doi":"10.1103/PhysRevE.87.063012","issue":"6","abstract":[{"lang":"eng","text":"In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers."}],"_id":"2811","author":[{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"},{"full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754"}],"title":"Nature of laminar-turbulence intermittency in shear flows","volume":87,"arxiv":1,"oa_version":"Preprint","month":"06","day":"18","citation":{"short":"M. Avila, B. Hof, Physical Review E 87 (2013).","ama":"Avila M, Hof B. Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. 2013;87(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>","ista":"Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 87(6), 063012.","ieee":"M. Avila and B. Hof, “Nature of laminar-turbulence intermittency in shear flows,” <i>Physical Review E</i>, vol. 87, no. 6. American Institute of Physics, 2013.","apa":"Avila, M., &#38; Hof, B. (2013). Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>","chicago":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>. American Institute of Physics, 2013. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>.","mla":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>, vol. 87, no. 6, 063012, American Institute of Physics, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4072","month":"06","citation":{"mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>, ACM, 2013, pp. 117–25, doi:<a href=\"https://doi.org/10.1145/2462356.2462373\">10.1145/2462356.2462373</a>.","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” In <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>, 117–25. ACM, 2013. <a href=\"https://doi.org/10.1145/2462356.2462373\">https://doi.org/10.1145/2462356.2462373</a>.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., &#38; Lieutier, A. (2013). Homological reconstruction and simplification in R3. In <i>Proceedings of the 29th annual symposium on Computational Geometry</i> (pp. 117–125). Rio de Janeiro, Brazil: ACM. <a href=\"https://doi.org/10.1145/2462356.2462373\">https://doi.org/10.1145/2462356.2462373</a>","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” in <i>Proceedings of the 29th annual symposium on Computational Geometry</i>, Rio de Janeiro, Brazil, 2013, pp. 117–125.","ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. In: <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>. ACM; 2013:117-125. doi:<a href=\"https://doi.org/10.1145/2462356.2462373\">10.1145/2462356.2462373</a>","short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, in:, Proceedings of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–125.","ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2013. Homological reconstruction and simplification in R3. Proceedings of the 29th annual symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 117–125."},"day":"01","department":[{"_id":"HeEd"}],"oa_version":"Submitted Version","date_created":"2018-12-11T11:59:44Z","scopus_import":1,"conference":{"location":"Rio de Janeiro, Brazil","start_date":"2013-06-17","end_date":"2013-06-20","name":"SoCG: Symposium on Computational Geometry"},"date_published":"2013-06-01T00:00:00Z","publisher":"ACM","main_file_link":[{"url":"http://hal.archives-ouvertes.fr/hal-00833791/","open_access":"1"}],"type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","_id":"2812","title":"Homological reconstruction and simplification in R3","oa":1,"author":[{"full_name":"Attali, Dominique","last_name":"Attali","first_name":"Dominique"},{"orcid":"0000-0002-9683-0724","last_name":"Bauer","full_name":"Bauer, Ulrich","first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Devillers","full_name":"Devillers, Olivier","first_name":"Olivier"},{"last_name":"Glisse","full_name":"Glisse, Marc","first_name":"Marc"},{"first_name":"André","last_name":"Lieutier","full_name":"Lieutier, André"}],"doi":"10.1145/2462356.2462373","abstract":[{"lang":"eng","text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard."}],"year":"2013","date_updated":"2023-02-23T10:15:15Z","publication":"Proceedings of the 29th annual symposium on Computational Geometry","page":"117 - 125","related_material":{"record":[{"status":"public","relation":"later_version","id":"1805"}]},"publication_status":"published","status":"public","acknowledgement":"Some of the authors were partially supported by the GIGA ANR grant (contract ANR-09-BLAN-0331-01) and the European project CG-Learning (contract 255827)."},{"_id":"2813","title":"Elasto-inertial turbulence","author":[{"last_name":"Samanta","full_name":"Samanta, Devranjan","first_name":"Devranjan"},{"full_name":"Dubief, Yves","last_name":"Dubief","first_name":"Yves"},{"last_name":"Holzner","full_name":"Holzner, Markus","first_name":"Markus"},{"first_name":"Christof","last_name":"Schäfer","full_name":"Schäfer, Christof"},{"first_name":"Alexander","full_name":"Morozov, Alexander","last_name":"Morozov"},{"full_name":"Wagner, Christian","last_name":"Wagner","first_name":"Christian"},{"last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"doi":"10.1073/pnas.1219666110","abstract":[{"lang":"eng","text":"Turbulence is ubiquitous in nature, yet even for the case of ordinary Newtonian fluids like water, our understanding of this phenomenon is limited. Many liquids of practical importance are more complicated (e.g., blood, polymer melts, paints), however; they exhibit elastic as well as viscous characteristics, and the relation between stress and strain is nonlinear. We demonstrate here for a model system of such complex fluids that at high shear rates, turbulence is not simply modified as previously believed but is suppressed and replaced by a different type of disordered motion, elasto-inertial turbulence. Elasto-inertial turbulence is found to occur at much lower Reynolds numbers than Newtonian turbulence, and the dynamical properties differ significantly. The friction scaling observed coincides with the so-called &quot;maximum drag reduction&quot; asymptote, which is exhibited by a wide range of viscoelastic fluids."}],"issue":"26","status":"public","publication_status":"published","month":"06","pmid":1,"citation":{"chicago":"Samanta, Devranjan, Yves Dubief, Markus Holzner, Christof Schäfer, Alexander Morozov, Christian Wagner, and Björn Hof. “Elasto-Inertial Turbulence.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1219666110\">https://doi.org/10.1073/pnas.1219666110</a>.","mla":"Samanta, Devranjan, et al. “Elasto-Inertial Turbulence.” <i>PNAS</i>, vol. 110, no. 26, National Academy of Sciences, 2013, pp. 10557–62, doi:<a href=\"https://doi.org/10.1073/pnas.1219666110\">10.1073/pnas.1219666110</a>.","apa":"Samanta, D., Dubief, Y., Holzner, M., Schäfer, C., Morozov, A., Wagner, C., &#38; Hof, B. (2013). Elasto-inertial turbulence. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1219666110\">https://doi.org/10.1073/pnas.1219666110</a>","ieee":"D. Samanta <i>et al.</i>, “Elasto-inertial turbulence,” <i>PNAS</i>, vol. 110, no. 26. National Academy of Sciences, pp. 10557–10562, 2013.","short":"D. Samanta, Y. Dubief, M. Holzner, C. Schäfer, A. Morozov, C. Wagner, B. Hof, PNAS 110 (2013) 10557–10562.","ama":"Samanta D, Dubief Y, Holzner M, et al. Elasto-inertial turbulence. <i>PNAS</i>. 2013;110(26):10557-10562. doi:<a href=\"https://doi.org/10.1073/pnas.1219666110\">10.1073/pnas.1219666110</a>","ista":"Samanta D, Dubief Y, Holzner M, Schäfer C, Morozov A, Wagner C, Hof B. 2013. Elasto-inertial turbulence. PNAS. 110(26), 10557–10562."},"day":"25","oa_version":"Submitted Version","volume":110,"oa":1,"year":"2013","date_updated":"2021-01-12T06:59:54Z","publication":"PNAS","page":"10557 - 10562","publist_id":"4073","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BjHo"}],"date_created":"2018-12-11T11:59:44Z","scopus_import":1,"date_published":"2013-06-25T00:00:00Z","external_id":{"pmid":["23757498"]},"publisher":"National Academy of Sciences","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696777/","open_access":"1"}],"intvolume":"       110","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1"}]