[{"language":[{"iso":"eng"}],"author":[{"last_name":"Matthee","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","orcid":"0000-0003-2871-127X"},{"first_name":"David","full_name":"Sobral, David","last_name":"Sobral"},{"first_name":"Iván","last_name":"Oteo","full_name":"Oteo, Iván"},{"last_name":"Best","full_name":"Best, Philip","first_name":"Philip"},{"first_name":"Ian","last_name":"Smail","full_name":"Smail, Ian"},{"first_name":"Huub","last_name":"Röttgering","full_name":"Röttgering, Huub"},{"first_name":"Ana","last_name":"Paulino-Afonso","full_name":"Paulino-Afonso, Ana"}],"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"date_updated":"2022-08-19T08:17:19Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present the first results from our CAlibrating LYMan α with Hα (CALYMHA) pilot survey at the Isaac Newton Telescope. We measure Lyα emission for 488 Hα selected galaxies at z = 2.23 from High-z Emission Line Survey in the COSMOS and UDS fields with a specially designed narrow-band filter (λc = 3918 Å, Δλ = 52 Å). We find 17 dual Hα-Lyα emitters [fLyα > 5 × 10−17 erg s−1 cm−2, of which five are X-ray active galactic nuclei (AGN)]. For star-forming galaxies, we find a range of Lyα escape fractions (fesc, measured with 3 arcsec apertures) from 2 to 30 per cent. These galaxies have masses from 3 × 108 M⊙ to 1011 M⊙ and dust attenuations E(B − V) = 0–0.5. Using stacking, we measure a median escape fraction of 1.6 ± 0.5 per cent (4.0 ± 1.0 per cent without correcting Hα for dust), but show that this depends on galaxy properties. The stacked fesc tends to decrease with increasing star formation rate and dust attenuation. However, at the highest masses and dust attenuations, we detect individual galaxies with fesc much higher than the typical values from stacking, indicating significant scatter in the values of fesc. Relations between fesc and UV slope are bimodal, with high fesc for either the bluest or reddest galaxies. We speculate that this bimodality and large scatter in the values of fesc is due to additional physical mechanisms such as outflows facilitating fesc for dusty/massive systems. Lyα is significantly more extended than Hα and the UV. fesc continues to increase up to at least 20 kpc (3σ, 40 kpc [2σ]) for typical star-forming galaxies and thus the aperture is the most important predictor of fesc.","lang":"eng"}],"volume":458,"year":"2016","scopus_import":"1","issue":"1","title":"The CALYMHA survey: Lyα escape fraction and its dependence on galaxy properties at z = 2.23","page":"449-467","article_type":"original","publisher":"Oxford University Press","_id":"11578","publication_status":"published","arxiv":1,"month":"05","quality_controlled":"1","acknowledgement":"We thank the anonymous referee for constructive comments and suggestions which have improved the quality of this work. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. DS and JM acknowledge financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship, and DS from FCT through a FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010) and from FCT grant PEst-OE/FIS/UI2751/2014. IO acknowledges support from the European Research Council (ERC) in the form of Advanced Investigator Programme, COSMICISM, 321302. HR acknowledges support from the ERC Advanced Investigator programme NewClusters 321271. IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson Merit Award. APA acknowledges support from the Fundac¸ao para a Ciencia e para a Tecnologia (FCT) through the Fellowship SFRH/BD/52706/2014.\r\nBased on observations made with the Isaac Newton Telescope (proposals 2013AN002, 2013BN008, 2014AC88, 2014AN002, 2014BN006, 2014BC118) operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrof´ısica de Canarias. We acknowledge the tremendous work that has been done by both COSMOS and UKIDSS UDS/SXDF teams in assembling such large, state-ofthe-art multi-wavelength data sets over such wide areas, as those have been crucial for the results presented in this paper. The sample of HAEs is publicly available from Sobral et al. (2013).\r\nWe have benefited greatly from the publically available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY (Jones et al. 2001; Hunter 2007; Van Der Walt, Colbert & Varoquaux 2011) and ASTROPY (Astropy Collaboration et al. 2013) packages, the imaging tools SEXTRACTOR, SWARP and SCAMP (Bertin & Arnouts 1996; Bertin 2006, 2010) and the TOPCAT analysis program (Taylor 2005).","type":"journal_article","publication":"Monthly Notices of the Royal Astronomical Society","date_created":"2022-07-14T08:51:37Z","citation":{"chicago":"Matthee, Jorryt J, David Sobral, Iván Oteo, Philip Best, Ian Smail, Huub Röttgering, and Ana Paulino-Afonso. “The CALYMHA Survey: Lyα Escape Fraction and Its Dependence on Galaxy Properties at z = 2.23.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/mnras/stw322\">https://doi.org/10.1093/mnras/stw322</a>.","ista":"Matthee JJ, Sobral D, Oteo I, Best P, Smail I, Röttgering H, Paulino-Afonso A. 2016. The CALYMHA survey: Lyα escape fraction and its dependence on galaxy properties at z = 2.23. Monthly Notices of the Royal Astronomical Society. 458(1), 449–467.","ieee":"J. J. Matthee <i>et al.</i>, “The CALYMHA survey: Lyα escape fraction and its dependence on galaxy properties at z = 2.23,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 458, no. 1. Oxford University Press, pp. 449–467, 2016.","short":"J.J. Matthee, D. Sobral, I. Oteo, P. Best, I. Smail, H. Röttgering, A. Paulino-Afonso, Monthly Notices of the Royal Astronomical Society 458 (2016) 449–467.","mla":"Matthee, Jorryt J., et al. “The CALYMHA Survey: Lyα Escape Fraction and Its Dependence on Galaxy Properties at z = 2.23.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 458, no. 1, Oxford University Press, 2016, pp. 449–67, doi:<a href=\"https://doi.org/10.1093/mnras/stw322\">10.1093/mnras/stw322</a>.","apa":"Matthee, J. J., Sobral, D., Oteo, I., Best, P., Smail, I., Röttgering, H., &#38; Paulino-Afonso, A. (2016). The CALYMHA survey: Lyα escape fraction and its dependence on galaxy properties at z = 2.23. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stw322\">https://doi.org/10.1093/mnras/stw322</a>","ama":"Matthee JJ, Sobral D, Oteo I, et al. The CALYMHA survey: Lyα escape fraction and its dependence on galaxy properties at z = 2.23. <i>Monthly Notices of the Royal Astronomical Society</i>. 2016;458(1):449-467. doi:<a href=\"https://doi.org/10.1093/mnras/stw322\">10.1093/mnras/stw322</a>"},"oa_version":"Preprint","day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02756"}],"extern":"1","external_id":{"arxiv":["1602.02756"]},"oa":1,"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","galaxies: ISM"],"intvolume":"       458","doi":"10.1093/mnras/stw322","date_published":"2016-05-01T00:00:00Z","status":"public"},{"oa":1,"day":"27","related_material":{"record":[{"status":"public","id":"9862","relation":"research_data"},{"status":"public","relation":"research_data","id":"9863"}]},"status":"public","article_number":"e2000234","doi":"10.1371/journal.pbio.2000234","date_published":"2016-12-27T00:00:00Z","intvolume":"        14","acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.","quality_controlled":"1","month":"12","pubrep_id":"742","citation":{"ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. 2016;14(12). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” <i>PLoS Biology</i>, vol. 14, no. 12. Public Library of Science, 2016.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234."},"oa_version":"Published Version","date_created":"2018-12-11T11:50:28Z","publication":"PLoS Biology","type":"journal_article","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","publication_status":"published","ddc":["576"],"file_date_updated":"2020-07-14T12:44:36Z","_id":"1158","publisher":"Public Library of Science","publist_id":"6200","abstract":[{"lang":"eng","text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate &quot;grey zone&quot; of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","content_type":"application/pdf","creator":"system","file_id":"5164","relation":"main_file","file_size":2494348,"date_created":"2018-12-12T10:15:42Z","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","date_updated":"2020-07-14T12:44:36Z","checksum":"2bab63b068a9840efd532b9ae583f9bb"}],"date_updated":"2023-02-23T14:11:16Z","author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"last_name":"Anciaux","full_name":"Anciaux, Youann","first_name":"Youann"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":1,"issue":"12","year":"2016","has_accepted_license":"1","volume":14},{"type":"conference","oa_version":"Preprint","citation":{"apa":"Fulek, R., Pelsmajer, M., &#38; Schaefer, M. (2016). Hanani-Tutte for radial planarity II (Vol. 9801, pp. 468–481). Presented at the GD: Graph Drawing and Network Visualization, Athens, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">https://doi.org/10.1007/978-3-319-50106-2_36</a>","mla":"Fulek, Radoslav, et al. <i>Hanani-Tutte for Radial Planarity II</i>. Vol. 9801, Springer, 2016, pp. 468–81, doi:<a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">10.1007/978-3-319-50106-2_36</a>.","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity II. In: Vol 9801. Springer; 2016:468-481. doi:<a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">10.1007/978-3-319-50106-2_36</a>","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity II,” 9801:468–81. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">https://doi.org/10.1007/978-3-319-50106-2_36</a>.","ista":"Fulek R, Pelsmajer M, Schaefer M. 2016. Hanani-Tutte for radial planarity II. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 468–481.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2016, pp. 468–481.","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity II,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp. 468–481."},"date_created":"2018-12-11T11:50:29Z","arxiv":1,"month":"12","quality_controlled":"1","date_published":"2016-12-08T00:00:00Z","doi":"10.1007/978-3-319-50106-2_36","intvolume":"      9801","status":"public","related_material":{"record":[{"relation":"later_version","id":"1113","status":"public"},{"status":"public","id":"1595","relation":"earlier_version"}]},"external_id":{"arxiv":["1608.08662"]},"day":"08","main_file_link":[{"url":"https://arxiv.org/abs/1608.08662","open_access":"1"}],"oa":1,"volume":9801,"scopus_import":1,"year":"2016","language":[{"iso":"eng"}],"conference":{"end_date":"2016-09-21","location":"Athens, Greece","name":"GD: Graph Drawing and Network Visualization","start_date":"2016-09-19"},"author":[{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","full_name":"Fulek, Radoslav","first_name":"Radoslav"},{"last_name":"Pelsmajer","full_name":"Pelsmajer, Michael","first_name":"Michael"},{"first_name":"Marcus","last_name":"Schaefer","full_name":"Schaefer, Marcus"}],"article_processing_charge":"No","date_updated":"2023-02-23T10:05:57Z","abstract":[{"lang":"eng","text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, … , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. A pair of edges e and f in a graph is independent if e and f do not share a vertex. We show that a graph G is radial planar if G has a radial drawing in which every two independent edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the strong Hanani-Tutte theorem for radial planarity. This characterization yields a very simple algorithm for radial planarity testing."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","publist_id":"6193","ec_funded":1,"_id":"1164","publication_status":"published","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"page":"468 - 481","title":"Hanani-Tutte for radial planarity II","alternative_title":["LNCS"],"department":[{"_id":"UlWa"}]},{"type":"conference","oa_version":"Preprint","citation":{"ama":"Fulek R. C-planarity of embedded cyclic c-graphs. In: Vol 9801. Springer; 2016:94-106. doi:<a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">10.1007/978-3-319-50106-2_8</a>","mla":"Fulek, Radoslav. <i>C-Planarity of Embedded Cyclic c-Graphs</i>. Vol. 9801, Springer, 2016, pp. 94–106, doi:<a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">10.1007/978-3-319-50106-2_8</a>.","apa":"Fulek, R. (2016). C-planarity of embedded cyclic c-graphs (Vol. 9801, pp. 94–106). Presented at the GD: Graph Drawing and Network Visualization, Athens, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">https://doi.org/10.1007/978-3-319-50106-2_8</a>","short":"R. Fulek, in:, Springer, 2016, pp. 94–106.","ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp. 94–106.","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs,” 9801:94–106. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">https://doi.org/10.1007/978-3-319-50106-2_8</a>.","ista":"Fulek R. 2016. C-planarity of embedded cyclic c-graphs. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 94–106."},"date_created":"2018-12-11T11:50:30Z","month":"12","quality_controlled":"1","acknowledgement":"R. Fulek—The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].\r\nI would like to thank Jan Kynčl and Dömötör Pálvölgyi for many comments and suggestions that helped to improve the presentation of the result.","date_published":"2016-12-08T00:00:00Z","doi":"10.1007/978-3-319-50106-2_8","status":"public","related_material":{"record":[{"relation":"later_version","id":"794","status":"public"}]},"main_file_link":[{"url":"https://arxiv.org/abs/1602.01346","open_access":"1"}],"day":"08","oa":1,"volume":"9801 ","scopus_import":1,"year":"2016","language":[{"iso":"eng"}],"author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774"}],"conference":{"name":"GD: Graph Drawing and Network Visualization","start_date":"2016-09-19","location":"Athens, Greece","end_date":"2016-09-21"},"date_updated":"2023-09-27T12:14:48Z","abstract":[{"lang":"eng","text":"We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","publist_id":"6192","ec_funded":1,"_id":"1165","publication_status":"published","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"page":"94 - 106","title":"C-planarity of embedded cyclic c-graphs","alternative_title":["LNCS"],"department":[{"_id":"UlWa"}]},{"abstract":[{"text":"Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph. However, it is unclear how these results translate to the biologically relevant case in which genotypes are represented by sequences of more than two units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the mutational graph is not the hypercube. Here we investigate accessibility of the best-adapted genotype in the general case of K &gt; 2 units. Using computer generated and experimental fitness landscapes we show that accessibility of the global fitness maximum increases with K and can be much higher than for binary sequences. The increase in accessibility comes from the increase in the number of indirect trajectories exploited by evolution for higher K. As one of the consequences, the fraction of genotypes that are accessible increases by three orders of magnitude when the number of units K increases from 2 to 16 for landscapes of size N ∼ 106genotypes. This suggests that evolution can follow many different trajectories on such landscapes and the reconstruction of evolutionary pathways from experimental data might be an extremely difficult task.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","file":[{"date_created":"2018-12-12T10:12:08Z","file_size":3822299,"creator":"system","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"4926","date_updated":"2020-07-14T12:44:37Z","file_name":"IST-2017-740-v1+1_journal.pcbi.1005218.pdf","checksum":"84f44ae92866c52ff1ca8a574558dca7"}],"date_updated":"2023-02-23T14:11:22Z","author":[{"orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski","full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Burda, Zdzisław","last_name":"Burda","first_name":"Zdzisław"},{"last_name":"Wacław","full_name":"Wacław, Bartłomiej","first_name":"Bartłomiej"}],"language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","issue":"12","year":"2016","has_accepted_license":"1","volume":12,"department":[{"_id":"AnKi"}],"title":"Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks","file_date_updated":"2020-07-14T12:44:37Z","publication_status":"published","ddc":["570"],"_id":"1167","publisher":"Public Library of Science","publist_id":"6190","acknowledgement":"MZ acknowledges the Polish National Science Centre grant no. DEC-2012/07/N/NZ2/00107. BW was supported by the Scottish Government/Royal Society of Edinburgh Personal Research Fellowship. We thank Marjon de Vos and Oliver Martin for critically reading the manuscript.","quality_controlled":"1","pubrep_id":"740","month":"12","oa_version":"Published Version","citation":{"mla":"Zagórski, Marcin P., et al. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” <i>PLoS Computational Biology</i>, vol. 12, no. 12, e1005218, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218\">10.1371/journal.pcbi.1005218</a>.","apa":"Zagórski, M. P., Burda, Z., &#38; Wacław, B. (2016). Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218\">https://doi.org/10.1371/journal.pcbi.1005218</a>","ama":"Zagórski MP, Burda Z, Wacław B. Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. <i>PLoS Computational Biology</i>. 2016;12(12). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218\">10.1371/journal.pcbi.1005218</a>","ista":"Zagórski MP, Burda Z, Wacław B. 2016. Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. 12(12), e1005218.","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” <i>PLoS Computational Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218\">https://doi.org/10.1371/journal.pcbi.1005218</a>.","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks,” <i>PLoS Computational Biology</i>, vol. 12, no. 12. Public Library of Science, 2016.","short":"M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016)."},"date_created":"2018-12-11T11:50:30Z","publication":"PLoS Computational Biology","type":"journal_article","oa":1,"day":"09","related_material":{"record":[{"status":"public","id":"9866","relation":"research_data"}]},"status":"public","article_number":"e1005218","date_published":"2016-12-09T00:00:00Z","doi":"10.1371/journal.pcbi.1005218","intvolume":"        12"},{"title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","department":[{"_id":"NiBa"}],"_id":"1172","publist_id":"6183","publisher":"Nature Publishing Group","publication_status":"published","ddc":["576"],"file_date_updated":"2020-07-14T12:44:37Z","author":[{"first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"},{"last_name":"Barma","full_name":"Barma, Mustansir","first_name":"Mustansir"},{"first_name":"Madan","full_name":"Rao, Madan","last_name":"Rao"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.","lang":"eng"}],"date_updated":"2021-01-12T06:48:50Z","file":[{"file_size":760967,"date_created":"2018-12-12T10:12:56Z","file_id":"4977","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"system","checksum":"cb378732da885ea4959ec5b845fb6e52","file_name":"IST-2017-737-v1+1_srep38840.pdf","date_updated":"2020-07-14T12:44:37Z"}],"has_accepted_license":"1","volume":6,"year":"2016","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":1,"oa":1,"day":"19","article_number":"38840","intvolume":"         6","date_published":"2016-12-19T00:00:00Z","doi":"10.1038/srep38840","status":"public","pubrep_id":"737","month":"12","acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","quality_controlled":"1","type":"journal_article","date_created":"2018-12-11T11:50:32Z","oa_version":"Published Version","citation":{"ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>.","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","apa":"Sachdeva, H., Barma, M., &#38; Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>","mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>, vol. 6, 38840, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>.","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>"},"publication":"Scientific Reports"},{"department":[{"_id":"KrPi"}],"main_file_link":[{"url":"http://eprint.iacr.org/2013/651","open_access":"1"}],"day":"01","page":"1321 - 1362","title":"A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound","oa":1,"status":"public","publication_status":"published","intvolume":"        74","publist_id":"6177","doi":"10.1007/s00453-015-9997-6","publisher":"Springer","date_published":"2016-04-01T00:00:00Z","_id":"1177","date_updated":"2021-01-12T06:48:52Z","quality_controlled":"1","acknowledgement":"We are grateful to the anonymous reviewers for their insightful comments. The\r\ndetailed reports helped us a lot to address the technical mistakes as well as to improve the overall presentation of the paper.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Boldyreva, Palacio and Warinschi introduced a multiple forking game as an extension of general forking. The notion of (multiple) forking is a useful abstraction from the actual simulation of cryptographic scheme to the adversary in a security reduction, and is achieved through the intermediary of a so-called wrapper algorithm. Multiple forking has turned out to be a useful tool in the security argument of several cryptographic protocols. However, a reduction employing multiple forking incurs a significant degradation of (Formula presented.) , where (Formula presented.) denotes the upper bound on the underlying random oracle calls and (Formula presented.) , the number of forkings. In this work we take a closer look at the reasons for the degradation with a tighter security bound in mind. We nail down the exact set of conditions for success in the multiple forking game. A careful analysis of the cryptographic schemes and corresponding security reduction employing multiple forking leads to the formulation of ‘dependence’ and ‘independence’ conditions pertaining to the output of the wrapper in different rounds. Based on the (in)dependence conditions we propose a general framework of multiple forking and a General Multiple Forking Lemma. Leveraging (in)dependence to the full allows us to improve the degradation factor in the multiple forking game by a factor of (Formula presented.). By implication, the cost of a single forking involving two random oracles (augmented forking) matches that involving a single random oracle (elementary forking). Finally, we study the effect of these observations on the concrete security of existing schemes employing multiple forking. We conclude that by careful design of the protocol (and the wrapper in the security reduction) it is possible to harness our observations to the full extent."}],"language":[{"iso":"eng"}],"month":"04","author":[{"first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg"},{"last_name":"Chatterjee","full_name":"Chatterjee, Sanjit","first_name":"Sanjit"}],"year":"2016","publication":"Algorithmica","issue":"4","date_created":"2018-12-11T11:50:33Z","citation":{"ama":"Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. <i>Algorithmica</i>. 2016;74(4):1321-1362. doi:<a href=\"https://doi.org/10.1007/s00453-015-9997-6\">10.1007/s00453-015-9997-6</a>","apa":"Kamath Hosdurg, C., &#38; Chatterjee, S. (2016). A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-015-9997-6\">https://doi.org/10.1007/s00453-015-9997-6</a>","mla":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” <i>Algorithmica</i>, vol. 74, no. 4, Springer, 2016, pp. 1321–62, doi:<a href=\"https://doi.org/10.1007/s00453-015-9997-6\">10.1007/s00453-015-9997-6</a>.","short":"C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362.","ieee":"C. Kamath Hosdurg and S. Chatterjee, “A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound,” <i>Algorithmica</i>, vol. 74, no. 4. Springer, pp. 1321–1362, 2016.","ista":"Kamath Hosdurg C, Chatterjee S. 2016. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. 74(4), 1321–1362.","chicago":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” <i>Algorithmica</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00453-015-9997-6\">https://doi.org/10.1007/s00453-015-9997-6</a>."},"oa_version":"Submitted Version","volume":74,"type":"journal_article"},{"conference":{"name":"TCC: Theory of Cryptography Conference","start_date":"2016-10-31","location":"Beijing, China","end_date":"2016-11-03"},"author":[{"orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Skorski","full_name":"Maciej, Skorski","last_name":"Maciej"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Computational notions of entropy have recently found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The two main types of results which make computational notions so useful are (1) Chain rules, which quantify by how much the computational entropy of a variable decreases if conditioned on some other variable (2) Transformations, which quantify to which extend one type of entropy implies another.\r\n\r\nSuch chain rules and transformations typically lose a significant amount in quality of the entropy, and are the reason why applying these results one gets rather weak quantitative security bounds. In this paper we for the first time prove lower bounds in this context, showing that existing results for transformations are, unfortunately, basically optimal for non-adaptive black-box reductions (and it’s hard to imagine how non black-box reductions or adaptivity could be useful here.)\r\n\r\nA variable X has k bits of HILL entropy of quality (ϵ,s)\r\nif there exists a variable Y with k bits min-entropy which cannot be distinguished from X with advantage ϵ\r\n\r\nby distinguishing circuits of size s. A weaker notion is Metric entropy, where we switch quantifiers, and only require that for every distinguisher of size s, such a Y exists.\r\n\r\nWe first describe our result concerning transformations. By definition, HILL implies Metric without any loss in quality. Metric entropy often comes up in applications, but must be transformed to HILL for meaningful security guarantees. The best known result states that if a variable X has k bits of Metric entropy of quality (ϵ,s)\r\n, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2). We show that this loss of a factor Ω(ϵ−2)\r\n\r\nin circuit size is necessary. In fact, we show the stronger result that this loss is already necessary when transforming so called deterministic real valued Metric entropy to randomised boolean Metric (both these variants of Metric entropy are implied by HILL without loss in quality).\r\n\r\nThe chain rule for HILL entropy states that if X has k bits of HILL entropy of quality (ϵ,s)\r\n, then for any variable Z of length m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still leaves a gap of ϵ between the known bound and our lower bound."}],"date_updated":"2021-01-12T06:48:53Z","volume":9985,"year":"2016","scopus_import":1,"title":"Pseudoentropy: Lower-bounds for chain rules and transformations","page":"183 - 203","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815"}],"department":[{"_id":"KrPi"}],"alternative_title":["LNCS"],"_id":"1179","ec_funded":1,"publist_id":"6175","publisher":"Springer","publication_status":"published","month":"10","acknowledgement":"K. Pietrzak—Supported by the European Research Council consolidator grant (682815-TOCNeT).\r\nM. Skórski—Supported by the National Science Center, Poland (2015/17/N/ST6/03564).","quality_controlled":"1","type":"conference","date_created":"2018-12-11T11:50:34Z","oa_version":"Preprint","citation":{"ista":"Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985, 183–203.","chicago":"Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">https://doi.org/10.1007/978-3-662-53641-4_8</a>.","short":"K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203.","ieee":"K. Z. Pietrzak and S. Maciej, “Pseudoentropy: Lower-bounds for chain rules and transformations,” presented at the TCC: Theory of Cryptography Conference, Beijing, China, 2016, vol. 9985, pp. 183–203.","mla":"Pietrzak, Krzysztof Z., and Skorski Maciej. <i>Pseudoentropy: Lower-Bounds for Chain Rules and Transformations</i>. Vol. 9985, Springer, 2016, pp. 183–203, doi:<a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">10.1007/978-3-662-53641-4_8</a>.","apa":"Pietrzak, K. Z., &#38; Maciej, S. (2016). Pseudoentropy: Lower-bounds for chain rules and transformations (Vol. 9985, pp. 183–203). Presented at the TCC: Theory of Cryptography Conference, Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">https://doi.org/10.1007/978-3-662-53641-4_8</a>","ama":"Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations. In: Vol 9985. Springer; 2016:183-203. doi:<a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">10.1007/978-3-662-53641-4_8</a>"},"oa":1,"day":"22","main_file_link":[{"url":"https://eprint.iacr.org/2016/159","open_access":"1"}],"intvolume":"      9985","date_published":"2016-10-22T00:00:00Z","doi":"10.1007/978-3-662-53641-4_8","status":"public"},{"publication_status":"published","related_material":{"link":[{"relation":"table_of_contents","url":"https://www.ijcai.org/proceedings/2016"}]},"status":"public","ec_funded":1,"_id":"1182","publisher":"AAAI Press","date_published":"2016-01-01T00:00:00Z","publist_id":"6171","department":[{"_id":"KrCh"}],"page":"172 - 179","title":"Robust draws in balanced knockout tournaments","oa":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.05090v1"}],"day":"01","oa_version":"Preprint","citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179.","mla":"Chatterjee, Krishnendu, et al. <i>Robust Draws in Balanced Knockout Tournaments</i>. Vol. 2016–January, AAAI Press, 2016, pp. 172–79.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Tkadlec, J. (2016). Robust draws in balanced knockout tournaments (Vol. 2016–January, pp. 172–179). Presented at the IJCAI: International Joint Conference on Artificial Intelligence, New York, NY, USA: AAAI Press.","short":"K. Chatterjee, R. Ibsen-Jensen, J. Tkadlec, in:, AAAI Press, 2016, pp. 172–179.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and J. Tkadlec, “Robust draws in balanced knockout tournaments,” presented at the IJCAI: International Joint Conference on Artificial Intelligence, New York, NY, USA, 2016, vol. 2016–January, pp. 172–179.","ista":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. 2016. Robust draws in balanced knockout tournaments. IJCAI: International Joint Conference on Artificial Intelligence vol. 2016–January, 172–179.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Josef Tkadlec. “Robust Draws in Balanced Knockout Tournaments,” 2016–January:172–79. AAAI Press, 2016."},"date_created":"2018-12-11T11:50:35Z","scopus_import":1,"year":"2016","type":"conference","volume":"2016-January","abstract":[{"text":"Balanced knockout tournaments are ubiquitous in sports competitions and are also used in decisionmaking and elections. The traditional computational question, that asks to compute a draw (optimal draw) that maximizes the winning probability for a distinguished player, has received a lot of attention. Previous works consider the problem where the pairwise winning probabilities are known precisely, while we study how robust is the winning probability with respect to small errors in the pairwise winning probabilities. First, we present several illuminating examples to establish: (a) there exist deterministic tournaments (where the pairwise winning probabilities are 0 or 1) where one optimal draw is much more robust than the other; and (b) in general, there exist tournaments with slightly suboptimal draws that are more robust than all the optimal draws. The above examples motivate the study of the computational problem of robust draws that guarantee a specified winning probability. Second, we present a polynomial-time algorithm for approximating the robustness of a draw for sufficiently small errors in pairwise winning probabilities, and obtain that the stated computational problem is NP-complete. We also show that two natural cases of deterministic tournaments where the optimal draw could be computed in polynomial time also admit polynomial-time algorithms to compute robust optimal draws.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-21T10:04:26Z","quality_controlled":"1","conference":{"start_date":"2016-07-09","location":"New York, NY, USA","name":"IJCAI: International Joint Conference on Artificial Intelligence","end_date":"2016-07-15"},"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-4783-0389","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","first_name":"Josef","orcid":"0000-0002-1097-9684"}],"month":"01","language":[{"iso":"eng"}]},{"publisher":"Cell Press","article_type":"original","publist_id":"6170","_id":"1183","file_date_updated":"2020-07-14T12:44:37Z","ddc":["576","616"],"publication_status":"published","project":[{"grant_number":"F03523","_id":"25473368-B435-11E9-9278-68D0E5697425","name":"Transmembrane Transporters in Health and Disease","call_identifier":"FWF"}],"title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","page":"1481 - 1494","department":[{"_id":"GaNo"}],"volume":167,"has_accepted_license":"1","issue":"6","scopus_import":"1","year":"2016","language":[{"iso":"eng"}],"author":[{"first_name":"Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","last_name":"Tarlungeanu","full_name":"Tarlungeanu, Dora-Clara"},{"orcid":"0000-0002-7370-5293","first_name":"Elena","full_name":"Deliu, Elena","last_name":"Deliu","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9033-9096","first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Majdi","full_name":"Kara, Majdi","last_name":"Kara"},{"full_name":"Janiesch, Philipp","last_name":"Janiesch","first_name":"Philipp"},{"first_name":"Mariafrancesca","full_name":"Scalise, Mariafrancesca","last_name":"Scalise"},{"first_name":"Michele","last_name":"Galluccio","full_name":"Galluccio, Michele"},{"full_name":"Tesulov, Mateja","last_name":"Tesulov","first_name":"Mateja"},{"first_name":"Emanuela","id":"3F4D1282-F248-11E8-B48F-1D18A9856A87","last_name":"Morelli","full_name":"Morelli, Emanuela"},{"first_name":"Fatma","last_name":"Sönmez","full_name":"Sönmez, Fatma"},{"full_name":"Bilgüvar, Kaya","last_name":"Bilgüvar","first_name":"Kaya"},{"first_name":"Ryuichi","full_name":"Ohgaki, Ryuichi","last_name":"Ohgaki"},{"first_name":"Yoshikatsu","last_name":"Kanai","full_name":"Kanai, Yoshikatsu"},{"first_name":"Anide","full_name":"Johansen, Anide","last_name":"Johansen"},{"full_name":"Esharif, Seham","last_name":"Esharif","first_name":"Seham"},{"first_name":"Tawfeg","last_name":"Ben Omran","full_name":"Ben Omran, Tawfeg"},{"first_name":"Meral","last_name":"Topcu","full_name":"Topcu, Meral"},{"first_name":"Avner","last_name":"Schlessinger","full_name":"Schlessinger, Avner"},{"first_name":"Cesare","full_name":"Indiveri, Cesare","last_name":"Indiveri"},{"first_name":"Kent","full_name":"Duncan, Kent","last_name":"Duncan"},{"full_name":"Caglayan, Ahmet","last_name":"Caglayan","first_name":"Ahmet"},{"last_name":"Günel","full_name":"Günel, Murat","first_name":"Murat"},{"last_name":"Gleeson","full_name":"Gleeson, Joseph","first_name":"Joseph"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia"}],"article_processing_charge":"No","file":[{"checksum":"7fe01ab12a6610d3db421e0136db2f77","file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","date_updated":"2020-07-14T12:44:37Z","file_size":73907957,"date_created":"2018-12-12T10:13:44Z","file_id":"5030","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"system"}],"date_updated":"2024-03-25T23:30:07Z","abstract":[{"text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2016-12-01T00:00:00Z","doi":"10.1016/j.cell.2016.11.013","intvolume":"       167","status":"public","related_material":{"record":[{"relation":"dissertation_contains","id":"395","status":"public"}]},"day":"01","oa":1,"type":"journal_article","publication":"Cell","citation":{"ieee":"D.-C. Tarlungeanu <i>et al.</i>, “Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder,” <i>Cell</i>, vol. 167, no. 6. Cell Press, pp. 1481–1494, 2016.","short":"D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise, M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai, A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri, K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494.","ista":"Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A, Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.","chicago":"Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>.","ama":"Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. 2016;167(6):1481-1494. doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>","apa":"Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise, M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>","mla":"Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>, vol. 167, no. 6, Cell Press, 2016, pp. 1481–94, doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>."},"oa_version":"Submitted Version","date_created":"2018-12-11T11:50:35Z","pubrep_id":"771","month":"12","quality_controlled":"1","acknowledgement":"This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu, and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900 to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.), the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We present a deterministic incremental algorithm for exactly maintaining the size of a minimum cut with ~O(1) amortized time per edge insertion and O(1) query time. This result partially answers an open question posed by Thorup [Combinatorica 2007]. It also stays in sharp contrast to a polynomial conditional lower-bound for the fully-dynamic weighted minimum cut problem. Our algorithm is obtained by combining a recent sparsification technique of Kawarabayashi and Thorup [STOC 2015] and an exact incremental algorithm of Henzinger [J. of Algorithm 1997].\r\n\r\nWe also study space-efficient incremental algorithms for the minimum cut problem. Concretely, we show that there exists an O(n log n/epsilon^2) space Monte-Carlo algorithm that can process a stream of edge insertions starting from an empty graph, and with high probability, the algorithm maintains a (1+epsilon)-approximation to the minimum cut. The algorithm has ~O(1) amortized update-time and constant query-time."}],"date_updated":"2023-02-16T12:05:59Z","article_processing_charge":"No","author":[{"first_name":"Gramoz","last_name":"Goranci","full_name":"Goranci, Gramoz"},{"orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Mikkel","last_name":"Thorup","full_name":"Thorup, Mikkel"}],"publication_identifier":{"isbn":["978-3-95977-015-6"],"issn":["1868-8969"]},"conference":{"name":"ESA: Annual European Symposium on Algorithms","start_date":"2016-08-22","location":"Aarhus, Denmark","end_date":"2016-08-24"},"language":[{"iso":"eng"}],"year":"2016","scopus_import":"1","volume":57,"alternative_title":["LIPIcs"],"title":"Incremental exact min-cut in poly-logarithmic amortized update time","publication_status":"published","_id":"11834","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","month":"08","arxiv":1,"date_created":"2022-08-12T10:58:32Z","citation":{"short":"G. Goranci, M.H. Henzinger, M. Thorup, in:, 24th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ieee":"G. Goranci, M. H. Henzinger, and M. Thorup, “Incremental exact min-cut in poly-logarithmic amortized update time,” in <i>24th Annual European Symposium on Algorithms</i>, Aarhus, Denmark, 2016, vol. 57.","chicago":"Goranci, Gramoz, Monika H Henzinger, and Mikkel Thorup. “Incremental Exact Min-Cut in Poly-Logarithmic Amortized Update Time.” In <i>24th Annual European Symposium on Algorithms</i>, Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPICS.ESA.2016.46\">https://doi.org/10.4230/LIPICS.ESA.2016.46</a>.","ista":"Goranci G, Henzinger MH, Thorup M. 2016. Incremental exact min-cut in poly-logarithmic amortized update time. 24th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 57, 46.","ama":"Goranci G, Henzinger MH, Thorup M. Incremental exact min-cut in poly-logarithmic amortized update time. In: <i>24th Annual European Symposium on Algorithms</i>. Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPICS.ESA.2016.46\">10.4230/LIPICS.ESA.2016.46</a>","apa":"Goranci, G., Henzinger, M. H., &#38; Thorup, M. (2016). Incremental exact min-cut in poly-logarithmic amortized update time. In <i>24th Annual European Symposium on Algorithms</i> (Vol. 57). Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.ESA.2016.46\">https://doi.org/10.4230/LIPICS.ESA.2016.46</a>","mla":"Goranci, Gramoz, et al. “Incremental Exact Min-Cut in Poly-Logarithmic Amortized Update Time.” <i>24th Annual European Symposium on Algorithms</i>, vol. 57, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPICS.ESA.2016.46\">10.4230/LIPICS.ESA.2016.46</a>."},"oa_version":"Published Version","publication":"24th Annual European Symposium on Algorithms","type":"conference","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPIcs.ESA.2016.46"}],"day":"18","external_id":{"arxiv":["1611.06500"]},"extern":"1","status":"public","article_number":"46","intvolume":"        57","doi":"10.4230/LIPICS.ESA.2016.46","date_published":"2016-08-18T00:00:00Z"},{"alternative_title":["LIPIcs"],"title":"Incremental and fully dynamic subgraph connectivity for emergency planning","publication_status":"published","_id":"11835","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"During the last 10 years it has become popular to study dynamic graph problems in a emergency planning or sensitivity setting: Instead of considering the general fully dynamic problem, we only have to process a single batch update of size d; after the update we have to answer queries.\r\n\r\nIn this paper, we consider the dynamic subgraph connectivity problem with sensitivity d: We are given a graph of which some vertices are activated and some are deactivated. After that we get a single update in which the states of up to $d$ vertices are changed. Then we get a sequence of connectivity queries in the subgraph of activated vertices.\r\n\r\nWe present the first fully dynamic algorithm for this problem which has an update and query time only slightly worse than the best decremental algorithm. In addition, we present the first incremental algorithm which is tight with respect to the best known conditional lower bound; moreover, the algorithm is simple and we believe it is implementable and efficient in practice.","lang":"eng"}],"date_updated":"2023-02-16T12:07:46Z","article_processing_charge":"No","publication_identifier":{"isbn":["978-3-95977-015-6"],"issn":["1868-8969"]},"author":[{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"full_name":"Neumann, Stefan","last_name":"Neumann","first_name":"Stefan"}],"conference":{"start_date":"2016-08-22","name":"ESA: Annual European Symposium on Algorithms","location":"Aarhus, Denmark","end_date":"2016-08-24"},"language":[{"iso":"eng"}],"year":"2016","scopus_import":"1","volume":57,"oa":1,"day":"18","main_file_link":[{"url":"https://doi.org/10.4230/LIPIcs.ESA.2016.48","open_access":"1"}],"external_id":{"arxiv":["1611.05248"]},"extern":"1","status":"public","article_number":"48","intvolume":"        57","doi":"10.4230/LIPICS.ESA.2016.48","date_published":"2016-08-18T00:00:00Z","quality_controlled":"1","month":"08","arxiv":1,"date_created":"2022-08-12T11:05:41Z","citation":{"ieee":"M. H. Henzinger and S. Neumann, “Incremental and fully dynamic subgraph connectivity for emergency planning,” in <i>24th Annual European Symposium on Algorithms</i>, Aarhus, Denmark, 2016, vol. 57.","short":"M.H. Henzinger, S. Neumann, in:, 24th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","chicago":"Henzinger, Monika H, and Stefan Neumann. “Incremental and Fully Dynamic Subgraph Connectivity for Emergency Planning.” In <i>24th Annual European Symposium on Algorithms</i>, Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPICS.ESA.2016.48\">https://doi.org/10.4230/LIPICS.ESA.2016.48</a>.","ista":"Henzinger MH, Neumann S. 2016. Incremental and fully dynamic subgraph connectivity for emergency planning. 24th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 57, 48.","ama":"Henzinger MH, Neumann S. Incremental and fully dynamic subgraph connectivity for emergency planning. In: <i>24th Annual European Symposium on Algorithms</i>. Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPICS.ESA.2016.48\">10.4230/LIPICS.ESA.2016.48</a>","apa":"Henzinger, M. H., &#38; Neumann, S. (2016). Incremental and fully dynamic subgraph connectivity for emergency planning. In <i>24th Annual European Symposium on Algorithms</i> (Vol. 57). Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.ESA.2016.48\">https://doi.org/10.4230/LIPICS.ESA.2016.48</a>","mla":"Henzinger, Monika H., and Stefan Neumann. “Incremental and Fully Dynamic Subgraph Connectivity for Emergency Planning.” <i>24th Annual European Symposium on Algorithms</i>, vol. 57, 48, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPICS.ESA.2016.48\">10.4230/LIPICS.ESA.2016.48</a>."},"oa_version":"Published Version","publication":"24th Annual European Symposium on Algorithms","type":"conference"},{"quality_controlled":"1","month":"08","arxiv":1,"date_created":"2022-08-12T11:16:01Z","citation":{"chicago":"Cheung, Yun Kuen, Gramoz Goranci, and Monika H Henzinger. “Graph Minors for Preserving Terminal Distances Approximately - Lower and Upper Bounds.” In <i>43rd International Colloquium on Automata, Languages, and Programming</i>, Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPICS.ICALP.2016.131\">https://doi.org/10.4230/LIPICS.ICALP.2016.131</a>.","ista":"Cheung YK, Goranci G, Henzinger MH. 2016. Graph minors for preserving terminal distances approximately - lower and upper bounds. 43rd International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 55, 131.","ieee":"Y. K. Cheung, G. Goranci, and M. H. Henzinger, “Graph minors for preserving terminal distances approximately - lower and upper bounds,” in <i>43rd International Colloquium on Automata, Languages, and Programming</i>, Rome, Italy, 2016, vol. 55.","short":"Y.K. Cheung, G. Goranci, M.H. Henzinger, in:, 43rd International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Cheung, Yun Kuen, et al. “Graph Minors for Preserving Terminal Distances Approximately - Lower and Upper Bounds.” <i>43rd International Colloquium on Automata, Languages, and Programming</i>, vol. 55, 131, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPICS.ICALP.2016.131\">10.4230/LIPICS.ICALP.2016.131</a>.","apa":"Cheung, Y. K., Goranci, G., &#38; Henzinger, M. H. (2016). Graph minors for preserving terminal distances approximately - lower and upper bounds. In <i>43rd International Colloquium on Automata, Languages, and Programming</i> (Vol. 55). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.ICALP.2016.131\">https://doi.org/10.4230/LIPICS.ICALP.2016.131</a>","ama":"Cheung YK, Goranci G, Henzinger MH. Graph minors for preserving terminal distances approximately - lower and upper bounds. In: <i>43rd International Colloquium on Automata, Languages, and Programming</i>. Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPICS.ICALP.2016.131\">10.4230/LIPICS.ICALP.2016.131</a>"},"oa_version":"Published Version","publication":"43rd International Colloquium on Automata, Languages, and Programming","type":"conference","oa":1,"day":"23","main_file_link":[{"url":"https://doi.org/10.4230/LIPICS.ICALP.2016.131","open_access":"1"}],"extern":"1","external_id":{"arxiv":["1604.08342"]},"status":"public","article_number":"131","intvolume":"        55","date_published":"2016-08-23T00:00:00Z","doi":"10.4230/LIPICS.ICALP.2016.131","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Given a graph where vertices are partitioned into k terminals and non-terminals, the goal is to compress the graph (i.e., reduce the number of non-terminals) using minor operations while preserving terminal distances approximately. The distortion of a compressed graph is the maximum multiplicative blow-up of distances between all pairs of terminals. We study the trade-off between the number of non-terminals and the distortion. This problem generalizes the Steiner Point Removal (SPR) problem, in which all non-terminals must be removed.\r\n\r\nWe introduce a novel black-box reduction to convert any lower bound on distortion for the SPR problem into a super-linear lower bound on the number of non-terminals, with the same distortion, for our problem. This allows us to show that there exist graphs such that every minor with distortion less than 2 / 2.5 / 3 must have Omega(k^2) / Omega(k^{5/4}) / Omega(k^{6/5}) non-terminals, plus more trade-offs in between. The black-box reduction has an interesting consequence: if the tight lower bound on distortion for the SPR problem is super-constant, then allowing any O(k) non-terminals will not help improving the lower bound to a constant.\r\n\r\nWe also build on the existing results on spanners, distance oracles and connected 0-extensions to show a number of upper bounds for general graphs, planar graphs, graphs that exclude a fixed minor and bounded treewidth graphs. Among others, we show that any graph admits a minor with O(log k) distortion and O(k^2) non-terminals, and any planar graph admits a minor with\r\n1 + epsilon distortion and ~O((k/epsilon)^2) non-terminals."}],"date_updated":"2023-02-16T12:09:54Z","article_processing_charge":"No","publication_identifier":{"isbn":["978-3-95977-013-2"],"issn":["1868-8969"]},"conference":{"start_date":"2016-07-12","location":"Rome, Italy","name":"ICALP: International Colloquium on Automata, Languages, and Programming","end_date":"2016-07-15"},"author":[{"first_name":"Yun Kuen","last_name":"Cheung","full_name":"Cheung, Yun Kuen"},{"first_name":"Gramoz","last_name":"Goranci","full_name":"Goranci, Gramoz"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"language":[{"iso":"eng"}],"year":"2016","scopus_import":"1","volume":55,"alternative_title":["LIPIcs"],"title":"Graph minors for preserving terminal distances approximately - lower and upper bounds","publication_status":"published","_id":"11836","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"24","scopus_import":1,"year":"2016","volume":6,"has_accepted_license":"1","file":[{"checksum":"789026eb9e1be2a0da08376f29f569cf","file_name":"IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf","date_updated":"2020-07-14T12:44:37Z","file_id":"5062","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"system","file_size":328414,"date_created":"2018-12-12T10:14:12Z"}],"date_updated":"2021-01-12T06:48:55Z","abstract":[{"lang":"eng","text":"Across multicellular organisms, the costs of reproduction and self-maintenance result in a life history trade-off between fecundity and longevity. Queens of perennial social Hymenoptera are both highly fertile and long-lived, and thus, this fundamental trade-off is lacking. Whether social insect males similarly evade the fecundity/longevity trade-off remains largely unstudied. Wingless males of the ant genus Cardiocondyla stay in their natal colonies throughout their relatively long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla obscurior males that were allowed to mate with large numbers of female sexuals had a shortened life span compared to males that mated at a low frequency or virgin males. Although frequent mating negatively affects longevity, males clearly benefit from a “live fast, die young strategy” by inseminating as many female sexuals as possible at a cost to their own survival."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","full_name":"Metzler, Sina","last_name":"Metzler"},{"first_name":"Jürgen","full_name":"Heinze, Jürgen","last_name":"Heinze"},{"full_name":"Schrempf, Alexandra","last_name":"Schrempf","first_name":"Alexandra"}],"publication_status":"published","file_date_updated":"2020-07-14T12:44:37Z","ddc":["576","592"],"publisher":"Wiley-Blackwell","publist_id":"6169","_id":"1184","department":[{"_id":"SyCr"}],"page":"8903 - 8906","title":"Mating and longevity in ant males","publication":"Ecology and Evolution","citation":{"ama":"Metzler S, Heinze J, Schrempf A. Mating and longevity in ant males. <i>Ecology and Evolution</i>. 2016;6(24):8903-8906. doi:<a href=\"https://doi.org/10.1002/ece3.2474\">10.1002/ece3.2474</a>","apa":"Metzler, S., Heinze, J., &#38; Schrempf, A. (2016). Mating and longevity in ant males. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.2474\">https://doi.org/10.1002/ece3.2474</a>","mla":"Metzler, Sina, et al. “Mating and Longevity in Ant Males.” <i>Ecology and Evolution</i>, vol. 6, no. 24, Wiley-Blackwell, 2016, pp. 8903–06, doi:<a href=\"https://doi.org/10.1002/ece3.2474\">10.1002/ece3.2474</a>.","ieee":"S. Metzler, J. Heinze, and A. Schrempf, “Mating and longevity in ant males,” <i>Ecology and Evolution</i>, vol. 6, no. 24. Wiley-Blackwell, pp. 8903–8906, 2016.","short":"S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906.","ista":"Metzler S, Heinze J, Schrempf A. 2016. Mating and longevity in ant males. Ecology and Evolution. 6(24), 8903–8906.","chicago":"Metzler, Sina, Jürgen Heinze, and Alexandra Schrempf. “Mating and Longevity in Ant Males.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1002/ece3.2474\">https://doi.org/10.1002/ece3.2474</a>."},"oa_version":"Published Version","date_created":"2018-12-11T11:50:36Z","type":"journal_article","quality_controlled":"1","acknowledgement":"German Science Foundation. Grant Number: SCHR 1135/2-1. We thank M. Adam for handling part of the setups and J. Zoellner for behavioral observations.","month":"12","pubrep_id":"736","status":"public","doi":"10.1002/ece3.2474","date_published":"2016-12-01T00:00:00Z","intvolume":"         6","day":"01","oa":1},{"oa":1,"day":"05","article_number":"38094","date_published":"2016-12-05T00:00:00Z","doi":"10.1038/srep38094","intvolume":"         6","status":"public","pubrep_id":"735","month":"12","acknowledgement":"We gratefully acknowledge Karsta Barnekow and Kristine Sievert-Giermann, for technical assistance and Lothar Petruschka for in silico analysis (all Dept. of Genetics, University of Greifswald). We are further grateful to the staff from SLS synchrotron beamline for help in data collection. This work was supported by grants from the Deutsche Forschungsgemeinschaft DFG GRK 1870 (to SH) and the Spanish Ministry of Economy and Competitiveness (BFU2014-59389-P to JAH, CTQ2014-52633-P to MB and SAF2012-39760-C02-02 to FG) and S2010/BMD-2457 (Community of Madrid to JAH and FG).","quality_controlled":"1","type":"journal_article","citation":{"ama":"Gutierrez-Fernandez J, Saleh M, Alcorlo M, et al. Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep38094\">10.1038/srep38094</a>","mla":"Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” <i>Scientific Reports</i>, vol. 6, 38094, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep38094\">10.1038/srep38094</a>.","apa":"Gutierrez-Fernandez, J., Saleh, M., Alcorlo, M., Gómez Mejóa, A., Pantoja Uceda, D., Treviño, M., … Hermoso, J. (2016). Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep38094\">https://doi.org/10.1038/srep38094</a>","short":"J. Gutierrez-Fernandez, M. Saleh, M. Alcorlo, A. Gómez Mejóa, D. Pantoja Uceda, M. Treviño, F. Vob, M. Abdullah, S. Galán Bartual, J. Seinen, P. Sánchez Murcia, F. Gago, M. Bruix, S. Hammerschmidt, J. Hermoso, Scientific Reports 6 (2016).","ieee":"J. Gutierrez-Fernandez <i>et al.</i>, “Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","chicago":"Gutierrez-Fernandez, Javier, Malek Saleh, Martín Alcorlo, Alejandro Gómez Mejóa, David Pantoja Uceda, Miguel Treviño, Franziska Vob, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep38094\">https://doi.org/10.1038/srep38094</a>.","ista":"Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gómez Mejóa A, Pantoja Uceda D, Treviño M, Vob F, Abdullah M, Galán Bartual S, Seinen J, Sánchez Murcia P, Gago F, Bruix M, Hammerschmidt S, Hermoso J. 2016. Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. 6, 38094."},"oa_version":"Published Version","date_created":"2018-12-11T11:50:36Z","publication":"Scientific Reports","title":"Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis","department":[{"_id":"LeSa"}],"_id":"1186","publisher":"Nature Publishing Group","publist_id":"6167","ddc":["576","610"],"file_date_updated":"2020-07-14T12:44:37Z","publication_status":"published","author":[{"full_name":"Gutierrez-Fernandez, Javier","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","last_name":"Gutierrez-Fernandez","first_name":"Javier"},{"full_name":"Saleh, Malek","last_name":"Saleh","first_name":"Malek"},{"first_name":"Martín","full_name":"Alcorlo, Martín","last_name":"Alcorlo"},{"full_name":"Gómez Mejóa, Alejandro","last_name":"Gómez Mejóa","first_name":"Alejandro"},{"last_name":"Pantoja Uceda","full_name":"Pantoja Uceda, David","first_name":"David"},{"full_name":"Treviño, Miguel","last_name":"Treviño","first_name":"Miguel"},{"full_name":"Vob, Franziska","last_name":"Vob","first_name":"Franziska"},{"last_name":"Abdullah","full_name":"Abdullah, Mohammed","first_name":"Mohammed"},{"full_name":"Galán Bartual, Sergio","last_name":"Galán Bartual","first_name":"Sergio"},{"last_name":"Seinen","full_name":"Seinen, Jolien","first_name":"Jolien"},{"last_name":"Sánchez Murcia","full_name":"Sánchez Murcia, Pedro","first_name":"Pedro"},{"first_name":"Federico","full_name":"Gago, Federico","last_name":"Gago"},{"full_name":"Bruix, Marta","last_name":"Bruix","first_name":"Marta"},{"first_name":"Sven","last_name":"Hammerschmidt","full_name":"Hammerschmidt, Sven"},{"first_name":"Juan","full_name":"Hermoso, Juan","last_name":"Hermoso"}],"language":[{"iso":"eng"}],"abstract":[{"text":"The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2017-735-v1+1_srep38094.pdf","date_updated":"2020-07-14T12:44:37Z","checksum":"e007d78b483bc59bf5ab98e9d42a6ec1","file_size":2716045,"date_created":"2018-12-12T10:10:18Z","content_type":"application/pdf","access_level":"open_access","creator":"system","file_id":"4804","relation":"main_file"}],"date_updated":"2021-01-12T06:48:56Z","has_accepted_license":"1","volume":6,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":1,"year":"2016"},{"extern":"1","external_id":{"arxiv":["1504.07056"]},"day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.07056"}],"oa":1,"date_published":"2016-06-01T00:00:00Z","doi":"10.1145/2897518.2897638","status":"public","arxiv":1,"month":"06","quality_controlled":"1","type":"conference","publication":"48th Annual ACM SIGACT Symposium on Theory of Computing","oa_version":"Preprint","citation":{"chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “A Deterministic Almost-Tight Distributed Algorithm for Approximating Single-Source Shortest Paths.” In <i>48th Annual ACM SIGACT Symposium on Theory of Computing</i>, 489–98. Association for Computing Machinery, 2016. <a href=\"https://doi.org/10.1145/2897518.2897638\">https://doi.org/10.1145/2897518.2897638</a>.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2016. A deterministic almost-tight distributed algorithm for approximating single-source shortest paths. 48th Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 489–498.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “A deterministic almost-tight distributed algorithm for approximating single-source shortest paths,” in <i>48th Annual ACM SIGACT Symposium on Theory of Computing</i>, Cambridge, MA, United States, 2016, pp. 489–498.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 48th Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp. 489–498.","apa":"Henzinger, M. H., Krinninger, S., &#38; Nanongkai, D. (2016). A deterministic almost-tight distributed algorithm for approximating single-source shortest paths. In <i>48th Annual ACM SIGACT Symposium on Theory of Computing</i> (pp. 489–498). Cambridge, MA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/2897518.2897638\">https://doi.org/10.1145/2897518.2897638</a>","mla":"Henzinger, Monika H., et al. “A Deterministic Almost-Tight Distributed Algorithm for Approximating Single-Source Shortest Paths.” <i>48th Annual ACM SIGACT Symposium on Theory of Computing</i>, Association for Computing Machinery, 2016, pp. 489–98, doi:<a href=\"https://doi.org/10.1145/2897518.2897638\">10.1145/2897518.2897638</a>.","ama":"Henzinger MH, Krinninger S, Nanongkai D. A deterministic almost-tight distributed algorithm for approximating single-source shortest paths. In: <i>48th Annual ACM SIGACT Symposium on Theory of Computing</i>. Association for Computing Machinery; 2016:489-498. doi:<a href=\"https://doi.org/10.1145/2897518.2897638\">10.1145/2897518.2897638</a>"},"date_created":"2022-08-16T09:19:31Z","page":"489 - 498","title":"A deterministic almost-tight distributed algorithm for approximating single-source shortest paths","publisher":"Association for Computing Machinery","_id":"11866","publication_status":"published","language":[{"iso":"eng"}],"conference":{"name":"STOC: Symposium on Theory of Computing","start_date":"2016-06-19","location":"Cambridge, MA, United States","end_date":"2016-06-21"},"author":[{"full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530"},{"full_name":"Krinninger, Sebastian","last_name":"Krinninger","first_name":"Sebastian"},{"full_name":"Nanongkai, Danupon","last_name":"Nanongkai","first_name":"Danupon"}],"publication_identifier":{"isbn":["978-145034132-5"],"issn":["0737-8017"]},"article_processing_charge":"No","date_updated":"2023-02-17T10:32:23Z","abstract":[{"lang":"eng","text":"We present a deterministic (1+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time algorithm for solving the single-source shortest paths problem on distributed weighted networks (the CONGEST model); here n is the number of nodes in the network and D is its (hop) diameter. This is the first non-trivial deterministic algorithm for this problem. It also improves (i) the running time of the randomized (1+o(1))-approximation Õ(n1/2D1/4+D)-time algorithm of Nanongkai [STOC 2014] by a factor of as large as n1/8, and (ii) the O(є−1logє−1)-approximation factor of Lenzen and Patt-Shamir’s Õ(n1/2+є+D)-time algorithm [STOC 2013] within the same running time. Our running time matches the known time lower bound of Ω(n1/2/logn + D) [Das Sarma et al. STOC 2011] modulo some lower-order terms, thus essentially settling the status of this problem which was raised at least a decade ago [Elkin SIGACT News 2004]. It also implies a (2+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time algorithm for approximating a network’s weighted diameter which almost matches the lower bound by Holzer et al. [PODC 2012].\r\n\r\nIn achieving this result, we develop two techniques which might be of independent interest and useful in other settings: (i) a deterministic process that replaces the “hitting set argument” commonly used for shortest paths computation in various settings, and (ii) a simple, deterministic, construction of an (no(1), o(1))-hop set of size O(n1+o(1)). We combine these techniques with many distributed algorithmic techniques, some of which from problems that are not directly related to shortest paths, e.g. ruling sets [Goldberg et al. STOC 1987], source detection [Lenzen, Peleg PODC 2013], and partial distance estimation [Lenzen, Patt-Shamir PODC 2015]. Our hop set construction also leads to single-source shortest paths algorithms in two other settings: (i) a (1+o(1))-approximation O(no(1))-time algorithm on congested cliques, and (ii) a (1+o(1))-approximation O(no(1)logW)-pass O(n1+o(1)logW)-space streaming algorithm, when edge weights are in {1, 2, …, W}. The first result answers an open problem in [Nanongkai, STOC 2014]. The second result partially answers an open problem raised by McGregor in 2006 [<pre>sublinear.info</pre>, Problem 14]."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","year":"2016"},{"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-145034132-5"],"issn":["0737-8017"]},"conference":{"location":"Cambridge, MA, United States","start_date":"2016-06-19","name":"STOC: Symposium on Theory of Computing","end_date":"2016-06-21"},"author":[{"full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya","first_name":"Sayan"},{"first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"}],"date_updated":"2023-02-17T11:08:19Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We present two deterministic dynamic algorithms for the maximum matching problem. (1) An algorithm that maintains a (2+є)-approximate maximum matching in general graphs with O(poly(logn, 1/є)) update time. (2) An algorithm that maintains an αK approximation of the value of the maximum matching with O(n2/K) update time in bipartite graphs, for every sufficiently large constant positive integer K. Here, 1≤ αK < 2 is a constant determined by the value of K. Result (1) is the first deterministic algorithm that can maintain an o(logn)-approximate maximum matching with polylogarithmic update time, improving the seminal result of Onak et al. [STOC 2010]. Its approximation guarantee almost matches the guarantee of the best randomized polylogarithmic update time algorithm [Baswana et al. FOCS 2011]. Result (2) achieves a better-than-two approximation with arbitrarily small polynomial update time on bipartite graphs. Previously the best update time for this problem was O(m1/4) [Bernstein et al. ICALP 2015], where m is the current number of edges in the graph."}],"year":"2016","scopus_import":"1","page":"398 - 411","title":"New deterministic approximation algorithms for fully dynamic matching","publisher":"Association for Computing Machinery","_id":"11867","publication_status":"published","arxiv":1,"month":"06","quality_controlled":"1","type":"conference","publication":"48th Annual ACM SIGACT Symposium on Theory of Computing","date_created":"2022-08-16T09:27:35Z","oa_version":"Preprint","citation":{"short":"S. Bhattacharya, M.H. Henzinger, D. Nanongkai, in:, 48th Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp. 398–411.","ieee":"S. Bhattacharya, M. H. Henzinger, and D. Nanongkai, “New deterministic approximation algorithms for fully dynamic matching,” in <i>48th Annual ACM SIGACT Symposium on Theory of Computing</i>, Cambridge, MA, United States, 2016, pp. 398–411.","ista":"Bhattacharya S, Henzinger MH, Nanongkai D. 2016. New deterministic approximation algorithms for fully dynamic matching. 48th Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 398–411.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, and Danupon Nanongkai. “New Deterministic Approximation Algorithms for Fully Dynamic Matching.” In <i>48th Annual ACM SIGACT Symposium on Theory of Computing</i>, 398–411. Association for Computing Machinery, 2016. <a href=\"https://doi.org/10.1145/2897518.2897568\">https://doi.org/10.1145/2897518.2897568</a>.","ama":"Bhattacharya S, Henzinger MH, Nanongkai D. New deterministic approximation algorithms for fully dynamic matching. In: <i>48th Annual ACM SIGACT Symposium on Theory of Computing</i>. Association for Computing Machinery; 2016:398-411. doi:<a href=\"https://doi.org/10.1145/2897518.2897568\">10.1145/2897518.2897568</a>","apa":"Bhattacharya, S., Henzinger, M. H., &#38; Nanongkai, D. (2016). New deterministic approximation algorithms for fully dynamic matching. In <i>48th Annual ACM SIGACT Symposium on Theory of Computing</i> (pp. 398–411). Cambridge, MA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/2897518.2897568\">https://doi.org/10.1145/2897518.2897568</a>","mla":"Bhattacharya, Sayan, et al. “New Deterministic Approximation Algorithms for Fully Dynamic Matching.” <i>48th Annual ACM SIGACT Symposium on Theory of Computing</i>, Association for Computing Machinery, 2016, pp. 398–411, doi:<a href=\"https://doi.org/10.1145/2897518.2897568\">10.1145/2897518.2897568</a>."},"day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1604.05765","open_access":"1"}],"external_id":{"arxiv":["1604.05765"]},"extern":"1","oa":1,"doi":"10.1145/2897518.2897568","date_published":"2016-06-01T00:00:00Z","status":"public"},{"acknowledgement":"D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night.","quality_controlled":"1","month":"12","oa_version":"Preprint","citation":{"short":"D. De Martino, D. Masoero,  Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).","ieee":"D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth,” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2016, no. 12. IOPscience, 2016.","ista":"De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth.  Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.","chicago":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &#38;amp; Growth.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience, 2016. <a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">https://doi.org/10.1088/1742-5468/aa4e8f</a>.","ama":"De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. 2016;2016(12). doi:<a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">10.1088/1742-5468/aa4e8f</a>","mla":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &#38;amp; Growth.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2016, no. 12, 123502, IOPscience, 2016, doi:<a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">10.1088/1742-5468/aa4e8f</a>.","apa":"De Martino, D., &#38; Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience. <a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">https://doi.org/10.1088/1742-5468/aa4e8f</a>"},"date_created":"2018-12-11T11:50:37Z","publication":" Journal of Statistical Mechanics: Theory and Experiment","type":"journal_article","oa":1,"day":"30","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.09048"}],"status":"public","article_number":"123502","date_published":"2016-12-30T00:00:00Z","doi":"10.1088/1742-5468/aa4e8f","intvolume":"      2016","abstract":[{"lang":"eng","text":"We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:57Z","author":[{"orcid":"0000-0002-5214-4706","first_name":"Daniele","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino"},{"first_name":"Davide","full_name":"Masoero, Davide","last_name":"Masoero"}],"language":[{"iso":"eng"}],"scopus_import":1,"issue":"12","year":"2016","volume":2016,"department":[{"_id":"GaTk"}],"title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"publication_status":"published","ec_funded":1,"_id":"1188","publisher":"IOPscience","publist_id":"6165"},{"page":"94","title":"Dissipative Few-Body Quantum Systems","oa":1,"day":"28","main_file_link":[{"open_access":"1","url":"http://repositum.tuwien.ac.at/obvutwhs/content/titleinfo/1517088"}],"extern":"1","supervisor":[{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"},{"last_name":"Rabl","full_name":"Rabl, Peter","first_name":"Peter"}],"_id":"1189","publist_id":"6164","date_published":"2016-11-28T00:00:00Z","publisher":"Technical University Vienna","publication_status":"published","status":"public","month":"11","author":[{"full_name":"Jochum, Clemens","last_name":"Jochum","first_name":"Clemens"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Within the scope of this thesis,  we show that a driven-dissipative system with\r\nfew ultracold atoms can exhibit dissipatively bound states, even if the atom-atom\r\ninteraction is purely repulsive.  This bond arises due to the dipole-dipole inter-\r\naction, which is restricted to one of the lower electronic energy states, resulting\r\nin the distance-dependent coherent population trapping.  The quality of this al-\r\nready established method of dissipative binding is improved and the application\r\nis extended to higher dimensions and a larger number of atoms.  Here, we simu-\r\nlate two- and three-atom systems using an adapted approach to the Monte Carlo\r\nwave-function  method  and  analyse  the  results.   Finally,  we  examine  the  possi-\r\nbility  of  finding  a  setting  allowing  trimer  states  but  prohibiting  dimer  states.\r\nIn the context of open quantum systems, such a three-body bound states corre-\r\nsponds to the driven-dissipative analogue of a Borromean state.  These states can\r\nbe detected in modern experiments with dipolar and Rydberg-dressed ultracold\r\natomic gases.\r\n"}],"date_updated":"2021-01-12T06:48:57Z","article_processing_charge":"No","type":"dissertation","date_created":"2018-12-11T11:50:37Z","citation":{"chicago":"Jochum, Clemens. “Dissipative Few-Body Quantum Systems.” Technical University Vienna, 2016.","ista":"Jochum C. 2016. Dissipative Few-Body Quantum Systems. Technical University Vienna.","ieee":"C. Jochum, “Dissipative Few-Body Quantum Systems,” Technical University Vienna, 2016.","short":"C. Jochum, Dissipative Few-Body Quantum Systems, Technical University Vienna, 2016.","apa":"Jochum, C. (2016). <i>Dissipative Few-Body Quantum Systems</i>. Technical University Vienna.","mla":"Jochum, Clemens. <i>Dissipative Few-Body Quantum Systems</i>. Technical University Vienna, 2016.","ama":"Jochum C. Dissipative Few-Body Quantum Systems. 2016."},"oa_version":"Published Version","year":"2016"},{"type":"journal_article","oa_version":"Preprint","citation":{"ista":"Henzinger MH, Krinninger S, Nanongkai D. 2016. Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. SIAM Journal on Computing. 45(3), 947–1006.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Dynamic Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.” <i>SIAM Journal on Computing</i>. Society for Industrial &#38; Applied Mathematics, 2016. <a href=\"https://doi.org/10.1137/140957299\">https://doi.org/10.1137/140957299</a>.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, SIAM Journal on Computing 45 (2016) 947–1006.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization,” <i>SIAM Journal on Computing</i>, vol. 45, no. 3. Society for Industrial &#38; Applied Mathematics, pp. 947–1006, 2016.","apa":"Henzinger, M. H., Krinninger, S., &#38; Nanongkai, D. (2016). Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. <i>SIAM Journal on Computing</i>. Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/140957299\">https://doi.org/10.1137/140957299</a>","mla":"Henzinger, Monika H., et al. “Dynamic Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.” <i>SIAM Journal on Computing</i>, vol. 45, no. 3, Society for Industrial &#38; Applied Mathematics, 2016, pp. 947–1006, doi:<a href=\"https://doi.org/10.1137/140957299\">10.1137/140957299</a>.","ama":"Henzinger MH, Krinninger S, Nanongkai D. Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. <i>SIAM Journal on Computing</i>. 2016;45(3):947-1006. doi:<a href=\"https://doi.org/10.1137/140957299\">10.1137/140957299</a>"},"date_created":"2022-08-17T08:37:00Z","publication":"SIAM Journal on Computing","month":"05","arxiv":1,"quality_controlled":"1","date_published":"2016-05-01T00:00:00Z","doi":"10.1137/140957299","intvolume":"        45","status":"public","oa":1,"extern":"1","external_id":{"arxiv":["1308.0776"]},"main_file_link":[{"url":"https://arxiv.org/abs/1308.0776","open_access":"1"}],"day":"01","volume":45,"scopus_import":"1","issue":"3","year":"2016","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"author":[{"first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"last_name":"Krinninger","full_name":"Krinninger, Sebastian","first_name":"Sebastian"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"}],"language":[{"iso":"eng"}],"abstract":[{"text":"We study dynamic (1+𝜖)-approximation algorithms for the all-pairs shortest paths problem in unweighted undirected 𝑛-node 𝑚-edge graphs under edge deletions. The fastest algorithm for this problem is a randomized algorithm with a total update time of 𝑂̃ (𝑚𝑛/𝜖) and constant query time by Roditty and Zwick [SIAM J. Comput., 41 (2012), pp. 670--683]. The fastest deterministic algorithm is from a 1981 paper by Even and Shiloach [J. ACM, 28 (1981), pp. 1--4]; it has a total update time of 𝑂(𝑚𝑛2) and constant query time. We improve these results as follows: (1) We present an algorithm with a total update time of 𝑂̃ (𝑛5/2/𝜖) and constant query time that has an additive error of 2 in addition to the 1+𝜖 multiplicative error. This beats the previous 𝑂̃ (𝑚𝑛/𝜖) time when 𝑚=Ω(𝑛3/2). Note that the additive error is unavoidable since, even in the static case, an 𝑂(𝑛3−𝛿)-time (a so-called truly subcubic) combinatorial algorithm with 1+𝜖 multiplicative error cannot have an additive error less than 2−𝜖, unless we make a major breakthrough for Boolean matrix multiplication [D. Dor, S. Halrepin, and U. Zwick, SIAM J. Comput., 29 (2000), pp. 1740--1759] and many other long-standing problems [V. Vassilevska Williams and R. Williams, Proceedings of the 2010 IEEE 51st Annual Symposium on Foundations of Computer Science, 2010, pp. 645--654]. The algorithm can also be turned into a (2+𝜖)-approximation algorithm (without an additive error) with the same time guarantees, improving the recent (3+𝜖)-approximation algorithm with 𝑂̃ (𝑛5/2+𝑂(log(1/𝜖)/log𝑛√)) running time of Bernstein and Roditty [Proceedings of the Twenty-Second Annual ACM-SIAM Symposium on Discrete Algorithms, 2011, pp. 1355--1365] in terms of both approximation and time guarantees. (2) We present a deterministic algorithm with a total update time of 𝑂̃ (𝑚𝑛/𝜖) and a query time of 𝑂(loglog𝑛). The algorithm has a multiplicative error of 1+𝜖 and gives the first improved deterministic algorithm since 1981. It also answers an open question raised by Bernstein in [Proceedings of the Forty-Fifth Annual ACM Symposium on Theory of Computing, 2013, pp. 725--734]. The deterministic algorithm can be turned into a deterministic fully dynamic (1+𝜖)-approximation with an amortized update time of 𝑂̃ (𝑚𝑛/(𝜖𝑡)) and a query time of 𝑂̃ (𝑡) for every 𝑡≤𝑛√. In order to achieve our results, we introduce two new techniques: (i) A monotone Even--Shiloach tree algorithm which maintains a bounded-distance shortest-paths tree on a certain type of emulator called a locally persevering emulator. (ii) A derandomization technique based on moving Even--Shiloach trees as a way to derandomize the standard random set argument. These techniques might be of independent interest.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2023-02-17T14:21:40Z","_id":"11891","publisher":"Society for Industrial & Applied Mathematics","article_type":"original","publication_status":"published","title":"Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization","page":"947-1006"}]