[{"oa_version":"Preprint","title":"Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation","author":[{"last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T.","last_name":"Michaels"},{"first_name":"Alessio","full_name":"Zaccone, Alessio","last_name":"Zaccone"},{"last_name":"Knowles","full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J."},{"first_name":"Daan","last_name":"Frenkel","full_name":"Frenkel, Daan"}],"day":"01","scopus_import":"1","article_type":"original","date_created":"2021-11-29T10:01:57Z","volume":145,"abstract":[{"text":"Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a process that has broad implications in many research areas ranging from medicine to nanotechnology. As such, spontaneous nucleation of protein fibrils has received much attention in recent years with many theoretical and experimental studies focusing on the underlying physical principles. In this paper we make a step forward in this direction and explore the early time behaviour of filamentous protein growth in the context of nucleation theory. We first provide an overview of the thermodynamics and kinetics of spontaneous nucleation of protein filaments in the presence of one relevant degree of freedom, namely the cluster size. In this case, we review how key kinetic observables, such as the reaction order of spontaneous nucleation, are directly related to the physical size of the critical nucleus. We then focus on the increasingly prominent case of filament nucleation that includes a conformational conversion of the nucleating building-block as an additional slow step in the nucleation process. Using computer simulations, we study the concentration dependence of the nucleation rate. We find that, under these circumstances, the reaction order of spontaneous nucleation with respect to the free monomer does no longer relate to the overall physical size of the nucleating aggregate but rather to the portion of the aggregate that actively participates in the conformational conversion. Our results thus provide a novel interpretation of the common kinetic descriptors of protein filament formation, including the reaction order of the nucleation step or the scaling exponent of lag times, and put into perspective current theoretical descriptions of protein aggregation.","lang":"eng"}],"intvolume":"       145","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"publication_status":"published","month":"12","arxiv":1,"article_number":"211926","language":[{"iso":"eng"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"21","citation":{"ista":"Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. 2016. Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. The Journal of Chemical Physics. 145(21), 211926.","chicago":"Šarić, Anđela, Thomas C. T. Michaels, Alessio Zaccone, Tuomas P. J. Knowles, and Daan Frenkel. “Kinetics of Spontaneous Filament Nucleation via Oligomers: Insights from Theory and Simulation.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4965040\">https://doi.org/10.1063/1.4965040</a>.","apa":"Šarić, A., Michaels, T. C. T., Zaccone, A., Knowles, T. P. J., &#38; Frenkel, D. (2016). Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. <i>The Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4965040\">https://doi.org/10.1063/1.4965040</a>","mla":"Šarić, Anđela, et al. “Kinetics of Spontaneous Filament Nucleation via Oligomers: Insights from Theory and Simulation.” <i>The Journal of Chemical Physics</i>, vol. 145, no. 21, 211926, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4965040\">10.1063/1.4965040</a>.","ama":"Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. <i>The Journal of Chemical Physics</i>. 2016;145(21). doi:<a href=\"https://doi.org/10.1063/1.4965040\">10.1063/1.4965040</a>","ieee":"A. Šarić, T. C. T. Michaels, A. Zaccone, T. P. J. Knowles, and D. Frenkel, “Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation,” <i>The Journal of Chemical Physics</i>, vol. 145, no. 21. American Institute of Physics, 2016.","short":"A. Šarić, T.C.T. Michaels, A. Zaccone, T.P.J. Knowles, D. Frenkel, The Journal of Chemical Physics 145 (2016)."},"publisher":"American Institute of Physics","doi":"10.1063/1.4965040","article_processing_charge":"No","type":"journal_article","date_updated":"2021-11-29T10:33:11Z","_id":"10376","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02320"}],"external_id":{"arxiv":["1610.02320"],"pmid":["28799382"]},"year":"2016","keyword":["physical and theoretical chemistry","general physics and astronomy"],"status":"public","publication":"The Journal of Chemical Physics","extern":"1","date_published":"2016-12-01T00:00:00Z","acknowledgement":"We acknowledge support from the Human Frontier Science Program and Emmanuel College (A.Š.), St John’s and Peterhouse Colleges (T.C.T.M.), the Swiss National Science Foundation (T.C.T.M.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council (T.C.T.M., T.P.J.K., and D.F.), and the Engineering and Physical Sciences Research Council (D.F.).","pmid":1},{"file_date_updated":"2021-11-29T10:50:00Z","publication_identifier":{"issn":["2045-2322"]},"publication_status":"published","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"         6","abstract":[{"lang":"eng","text":"The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself mediates protein self-organization in these processes through minimization of membrane curvature energy. Here, we present a combined experimental and numerical study in which we quantify these interactions directly for the first time. In our experimental model system we control the deformation of a lipid membrane by adhering colloidal particles. Using confocal microscopy, we establish that these membrane deformations cause an attractive interaction force leading to reversible binding. The attraction extends over 2.5 times the particle diameter and has a strength of three times the thermal energy (−3.3 kBT). Coarse-grained Monte-Carlo simulations of the system are in excellent agreement with the experimental results and prove that the measured interaction is independent of length scale. Our combined experimental and numerical results reveal membrane curvature as a common physical origin for interactions between any membrane-deforming objects, from nanometre-sized proteins to micrometre-sized particles."}],"volume":6,"date_created":"2021-11-29T10:34:08Z","article_type":"original","day":"13","scopus_import":"1","author":[{"first_name":"Casper","full_name":"van der Wel, Casper","last_name":"van der Wel"},{"first_name":"Afshin","last_name":"Vahid","full_name":"Vahid, Afshin"},{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139"},{"last_name":"Idema","full_name":"Idema, Timon","first_name":"Timon"},{"first_name":"Doris","full_name":"Heinrich, Doris","last_name":"Heinrich"},{"first_name":"Daniela J.","last_name":"Kraft","full_name":"Kraft, Daniela J."}],"title":"Lipid membrane-mediated attraction between curvature inducing objects","oa_version":"Published Version","citation":{"short":"C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, D.J. Kraft, Scientific Reports 6 (2016).","ieee":"C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, and D. J. Kraft, “Lipid membrane-mediated attraction between curvature inducing objects,” <i>Scientific Reports</i>, vol. 6, no. 1. Springer Nature, 2016.","ama":"van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. Lipid membrane-mediated attraction between curvature inducing objects. <i>Scientific Reports</i>. 2016;6(1). doi:<a href=\"https://doi.org/10.1038/srep32825\">10.1038/srep32825</a>","mla":"van der Wel, Casper, et al. “Lipid Membrane-Mediated Attraction between Curvature Inducing Objects.” <i>Scientific Reports</i>, vol. 6, no. 1, 32825, Springer Nature, 2016, doi:<a href=\"https://doi.org/10.1038/srep32825\">10.1038/srep32825</a>.","apa":"van der Wel, C., Vahid, A., Šarić, A., Idema, T., Heinrich, D., &#38; Kraft, D. J. (2016). Lipid membrane-mediated attraction between curvature inducing objects. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/srep32825\">https://doi.org/10.1038/srep32825</a>","chicago":"Wel, Casper van der, Afshin Vahid, Anđela Šarić, Timon Idema, Doris Heinrich, and Daniela J. Kraft. “Lipid Membrane-Mediated Attraction between Curvature Inducing Objects.” <i>Scientific Reports</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/srep32825\">https://doi.org/10.1038/srep32825</a>.","ista":"van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. 2016. Lipid membrane-mediated attraction between curvature inducing objects. Scientific Reports. 6(1), 32825."},"issue":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","date_updated":"2021-11-29T10:50:00Z","date_created":"2021-11-29T10:50:00Z","file_size":1598289,"file_id":"10379","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2016_SciRep_vanderWel.pdf","checksum":"d6cf16dd511e15726b001e7cc287cf1d","relation":"main_file"}],"article_number":"32825","arxiv":1,"month":"09","main_file_link":[{"open_access":"1","url":"https://www.nature.com/articles/srep32825"}],"quality_controlled":"1","ddc":["540"],"_id":"10377","date_updated":"2021-11-29T11:08:15Z","type":"journal_article","article_processing_charge":"No","doi":"10.1038/srep32825","publisher":"Springer Nature","pmid":1,"date_published":"2016-09-13T00:00:00Z","acknowledgement":"This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program and VENI grant 680-47-431. We thank Jeroen Appel and Wim Pomp for advice on the protocol design and Marcel Winter and Ruben Verweij for experimental support.","status":"public","extern":"1","publication":"Scientific Reports","keyword":["multidisciplinary"],"year":"2016","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/srep37382"}]},"external_id":{"arxiv":["1603.04644"],"pmid":["27618764"]}},{"month":"07","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"9","citation":{"mla":"Šarić, Anđela, et al. “Physical Determinants of the Self-Replication of Protein Fibrils.” <i>Nature Physics</i>, vol. 12, no. 9, Springer Nature, 2016, pp. 874–80, doi:<a href=\"https://doi.org/10.1038/nphys3828\">10.1038/nphys3828</a>.","apa":"Šarić, A., Buell, A. K., Meisl, G., Michaels, T. C. T., Dobson, C. M., Linse, S., … Frenkel, D. (2016). Physical determinants of the self-replication of protein fibrils. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nphys3828\">https://doi.org/10.1038/nphys3828</a>","ista":"Šarić A, Buell AK, Meisl G, Michaels TCT, Dobson CM, Linse S, Knowles TPJ, Frenkel D. 2016. Physical determinants of the self-replication of protein fibrils. Nature Physics. 12(9), 874–880.","chicago":"Šarić, Anđela, Alexander K. Buell, Georg Meisl, Thomas C. T. Michaels, Christopher M. Dobson, Sara Linse, Tuomas P. J. Knowles, and Daan Frenkel. “Physical Determinants of the Self-Replication of Protein Fibrils.” <i>Nature Physics</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/nphys3828\">https://doi.org/10.1038/nphys3828</a>.","short":"A. Šarić, A.K. Buell, G. Meisl, T.C.T. Michaels, C.M. Dobson, S. Linse, T.P.J. Knowles, D. Frenkel, Nature Physics 12 (2016) 874–880.","ieee":"A. Šarić <i>et al.</i>, “Physical determinants of the self-replication of protein fibrils,” <i>Nature Physics</i>, vol. 12, no. 9. Springer Nature, pp. 874–880, 2016.","ama":"Šarić A, Buell AK, Meisl G, et al. Physical determinants of the self-replication of protein fibrils. <i>Nature Physics</i>. 2016;12(9):874-880. doi:<a href=\"https://doi.org/10.1038/nphys3828\">10.1038/nphys3828</a>"},"language":[{"iso":"eng"}],"oa":1,"article_type":"original","date_created":"2021-11-29T10:36:11Z","volume":12,"title":"Physical determinants of the self-replication of protein fibrils","oa_version":"Preprint","author":[{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139"},{"first_name":"Alexander K.","full_name":"Buell, Alexander K.","last_name":"Buell"},{"first_name":"Georg","full_name":"Meisl, Georg","last_name":"Meisl"},{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"last_name":"Dobson","full_name":"Dobson, Christopher M.","first_name":"Christopher M."},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"},{"last_name":"Frenkel","full_name":"Frenkel, Daan","first_name":"Daan"}],"day":"18","scopus_import":"1","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publication_status":"published","intvolume":"        12","abstract":[{"text":"The ability of biological molecules to replicate themselves is the foundation of life, requiring a complex cellular machinery. However, a range of aberrant processes involve the self-replication of pathological protein structures without any additional assistance. One example is the autocatalytic generation of pathological protein aggregates, including amyloid fibrils, involved in neurodegenerative disorders. Here, we use computer simulations to identify the necessary requirements for the self-replication of fibrillar assemblies of proteins. We establish that a key physical determinant for this process is the affinity of proteins for the surfaces of fibrils. We find that self-replication can take place only in a very narrow regime of inter-protein interactions, implying a high level of sensitivity to system parameters and experimental conditions. We then compare our theoretical predictions with kinetic and biosensor measurements of fibrils formed from the Aβ peptide associated with Alzheimer’s disease. Our results show a quantitative connection between the kinetics of self-replication and the surface coverage of fibrils by monomeric proteins. These findings reveal the fundamental physical requirements for the formation of supra-molecular structures able to replicate themselves, and shed light on mechanisms in play in the proliferation of protein aggregates in nature.","lang":"eng"}],"keyword":["general physics and astronomy"],"external_id":{"pmid":["31031819"]},"year":"2016","date_published":"2016-07-18T00:00:00Z","acknowledgement":"We acknowledge support from the Human Frontier Science Program and Emmanuel College (A.Š.), the Leverhulme Trust and Magdalene College (A.K.B.), St John’s College (T.C.T.M.), the Biotechnology and Biological Sciences Research Council (T.P.J.K. and C.M.D.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council (T.P.J.K., T.C.T.M., S.L. and D.F.), and the Engineering and Physical Sciences Research Council (D.F.).","pmid":1,"publication":"Nature Physics","extern":"1","status":"public","type":"journal_article","date_updated":"2021-11-29T11:07:25Z","_id":"10378","publisher":"Springer Nature","doi":"10.1038/nphys3828","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://discovery.ucl.ac.uk/id/eprint/1517406/"}],"page":"874-880"},{"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1602.02734","open_access":"1"}],"publisher":"American Institute of Physics","article_processing_charge":"No","doi":"10.1063/1.4953036","type":"journal_article","_id":"10380","date_updated":"2021-11-29T13:09:08Z","status":"public","extern":"1","publication":"The Journal of Chemical Physics","date_published":"2016-06-10T00:00:00Z","acknowledgement":"The authors should like to dedicate this paper to the memory of Simon de Leeuw, who was a pioneer in the calculation of Coulomb effects in simulations. P.W. would like to thank the Austrian Academy of Sciences for financial support through a DOC Fellowship, and for covering the travel expenses for the CECAM workshop in Zaragoza in May 2015, where these results were first presented. P.W. would also like to thank Chao Zhang for pointing out the equivalence of the two expressions for the electric field discussed in Sec. VI D, Michiel Sprik for emphasising the importance of the quadrupole contribution in experimental studies of interfacial systems, as well as Aleks Reinhardt and other members of the Frenkel and Dellago groups for their advice. We further acknowledge support from the Federation of Austrian Industry (IV) Carinthia (P.W.), the University of Zagreb and Erasmus SMP (D. Fijan), the Human Frontier Science Program and Emmanuel College (A.Š.), the Austrian Science Fund FWF within the SFB Vicom project F41 (C.D.), and the Engineering and Physical Sciences Research Council Programme Grant No. EP/I001352/1 (D.F.). Additional data related to this publication are available at the University of Cambridge data repository (http://dx.doi.org/10.17863/CAM.118).","pmid":1,"external_id":{"arxiv":["1602.02734"],"pmid":["27305991"]},"year":"2016","keyword":["physical and theoretical chemistry","general physics and astronomy"],"intvolume":"       144","abstract":[{"text":"Using non-equilibrium molecular dynamics simulations, it has been recently demonstrated that water molecules align in response to an imposed temperature gradient, resulting in an effective electric field. Here, we investigate how thermally induced fields depend on the underlying treatment of long-ranged interactions. For the short-ranged Wolf method and Ewald summation, we find the peak strength of the field to range between 2 × 107 and 5 × 107 V/m for a temperature gradient of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139, 014504 (2013); J. Armstrong et al., J. Chem. Phys. 143, 036101 (2015)]. We show that this discrepancy can be traced back to the use of an incorrect kernel in the calculation of the electrostatic field. More seriously, we find that the Wolf method fails to predict correct molecular orientations, resulting in dipole densities with opposite sign to those computed using Ewald summation. By considering two different multipole expansions, we show that, for inhomogeneous polarisations, the quadrupole contribution can be significant and even outweigh the dipole contribution to the field. Finally, we propose a more accurate way of calculating the electrostatic potential and the field. In particular, we show that averaging the microscopic field analytically to obtain the macroscopic Maxwell field reduces the error bars by up to an order of magnitude. As a consequence, the simulation times required to reach a given statistical accuracy decrease by up to two orders of magnitude.","lang":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"title":"Non-equilibrium simulations of thermally induced electric fields in water","oa_version":"Preprint","day":"10","scopus_import":"1","author":[{"first_name":"P.","full_name":"Wirnsberger, P.","last_name":"Wirnsberger"},{"last_name":"Fijan","full_name":"Fijan, D.","first_name":"D."},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"first_name":"M.","last_name":"Neumann","full_name":"Neumann, M."},{"full_name":"Dellago, C.","last_name":"Dellago","first_name":"C."},{"last_name":"Frenkel","full_name":"Frenkel, D.","first_name":"D."}],"date_created":"2021-11-29T11:08:52Z","article_type":"original","volume":144,"language":[{"iso":"eng"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The Journal of Chemical Physics 144 (2016).","ieee":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, and D. Frenkel, “Non-equilibrium simulations of thermally induced electric fields in water,” <i>The Journal of Chemical Physics</i>, vol. 144, no. 22. American Institute of Physics, 2016.","ama":"Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium simulations of thermally induced electric fields in water. <i>The Journal of Chemical Physics</i>. 2016;144(22). doi:<a href=\"https://doi.org/10.1063/1.4953036\">10.1063/1.4953036</a>","mla":"Wirnsberger, P., et al. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” <i>The Journal of Chemical Physics</i>, vol. 144, no. 22, 224102, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4953036\">10.1063/1.4953036</a>.","apa":"Wirnsberger, P., Fijan, D., Šarić, A., Neumann, M., Dellago, C., &#38; Frenkel, D. (2016). Non-equilibrium simulations of thermally induced electric fields in water. <i>The Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4953036\">https://doi.org/10.1063/1.4953036</a>","chicago":"Wirnsberger, P., D. Fijan, Anđela Šarić, M. Neumann, C. Dellago, and D. Frenkel. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4953036\">https://doi.org/10.1063/1.4953036</a>.","ista":"Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. 2016. Non-equilibrium simulations of thermally induced electric fields in water. The Journal of Chemical Physics. 144(22), 224102."},"issue":"22","arxiv":1,"month":"06","article_number":"224102"},{"type":"journal_article","date_updated":"2021-11-29T13:09:00Z","_id":"10381","publisher":"Royal Society of Chemistry","doi":"10.1039/c6sm01515h","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1608.05788","open_access":"1"}],"page":"7804-7817","keyword":["condensed matter physics","general chemistry"],"external_id":{"arxiv":["1608.05788"],"pmid":["27722701"]},"year":"2016","date_published":"2016-08-19T00:00:00Z","pmid":1,"extern":"1","publication":"Soft Matter","status":"public","article_type":"original","date_created":"2021-11-29T11:09:55Z","volume":12,"oa_version":"Preprint","title":"Melting transition in lipid vesicles functionalised by mobile DNA linkers","author":[{"first_name":"Stephan Jan","full_name":"Bachmann, Stephan Jan","last_name":"Bachmann"},{"first_name":"Jurij","last_name":"Kotar","full_name":"Kotar, Jurij"},{"first_name":"Lucia","last_name":"Parolini","full_name":"Parolini, Lucia"},{"last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"full_name":"Cicuta, Pietro","last_name":"Cicuta","first_name":"Pietro"},{"first_name":"Lorenzo","last_name":"Di Michele","full_name":"Di Michele, Lorenzo"},{"full_name":"Mognetti, Bortolo Matteo","last_name":"Mognetti","first_name":"Bortolo Matteo"}],"scopus_import":"1","day":"19","publication_status":"published","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"abstract":[{"lang":"eng","text":"We study phase behaviour of lipid-bilayer vesicles functionalised by ligand–receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo simulations that combine a coarse grained description of the lipid bilayer with state of art analytical models for multivalent ligand–receptor interactions. Using density of state calculations, we derive the partition function in pairs of vesicles and compute the number of ligand–receptor bonds as a function of temperature. Numerical results are compared to microscopy and fluorimetry experiments on large unilamellar vesicles decorated by DNA linkers carrying complementary overhangs. We find that vesicle aggregation is suppressed when the total number of linkers falls below a threshold value. Within the model proposed here, this is due to the higher configurational costs required to form inter-vesicle bridges as compared to intra-vesicle loops, which are in turn related to membrane deformability. Our findings and our numerical/experimental methodologies are applicable to the rational design of liposomes used as functional materials and drug delivery applications, as well as to study inter-membrane interactions in living systems, such as cell adhesion."}],"intvolume":"        12","month":"08","arxiv":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"37","citation":{"short":"S.J. Bachmann, J. Kotar, L. Parolini, A. Šarić, P. Cicuta, L. Di Michele, B.M. Mognetti, Soft Matter 12 (2016) 7804–7817.","ieee":"S. J. Bachmann <i>et al.</i>, “Melting transition in lipid vesicles functionalised by mobile DNA linkers,” <i>Soft Matter</i>, vol. 12, no. 37. Royal Society of Chemistry, pp. 7804–7817, 2016.","ama":"Bachmann SJ, Kotar J, Parolini L, et al. Melting transition in lipid vesicles functionalised by mobile DNA linkers. <i>Soft Matter</i>. 2016;12(37):7804-7817. doi:<a href=\"https://doi.org/10.1039/c6sm01515h\">10.1039/c6sm01515h</a>","mla":"Bachmann, Stephan Jan, et al. “Melting Transition in Lipid Vesicles Functionalised by Mobile DNA Linkers.” <i>Soft Matter</i>, vol. 12, no. 37, Royal Society of Chemistry, 2016, pp. 7804–17, doi:<a href=\"https://doi.org/10.1039/c6sm01515h\">10.1039/c6sm01515h</a>.","apa":"Bachmann, S. J., Kotar, J., Parolini, L., Šarić, A., Cicuta, P., Di Michele, L., &#38; Mognetti, B. M. (2016). Melting transition in lipid vesicles functionalised by mobile DNA linkers. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c6sm01515h\">https://doi.org/10.1039/c6sm01515h</a>","ista":"Bachmann SJ, Kotar J, Parolini L, Šarić A, Cicuta P, Di Michele L, Mognetti BM. 2016. Melting transition in lipid vesicles functionalised by mobile DNA linkers. Soft Matter. 12(37), 7804–7817.","chicago":"Bachmann, Stephan Jan, Jurij Kotar, Lucia Parolini, Anđela Šarić, Pietro Cicuta, Lorenzo Di Michele, and Bortolo Matteo Mognetti. “Melting Transition in Lipid Vesicles Functionalised by Mobile DNA Linkers.” <i>Soft Matter</i>. Royal Society of Chemistry, 2016. <a href=\"https://doi.org/10.1039/c6sm01515h\">https://doi.org/10.1039/c6sm01515h</a>."},"language":[{"iso":"eng"}],"oa":1},{"year":"2016","month":"02","publist_id":"6331","extern":"1","language":[{"iso":"eng"}],"status":"public","publication":"Nature Photonics","citation":{"apa":"Danzl, J. G., Sidenstein, S., Gregor, C., Urban, N., Ilgen, P., Jakobs, S., &#38; Hell, S. (2016). Coordinate-targeted fluorescence nanoscopy with multiple off states. <i>Nature Photonics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphoton.2015.266\">https://doi.org/10.1038/nphoton.2015.266</a>","mla":"Danzl, Johann G., et al. “Coordinate-Targeted Fluorescence Nanoscopy with Multiple off States.” <i>Nature Photonics</i>, vol. 10, no. 2, Nature Publishing Group, 2016, pp. 122–28, doi:<a href=\"https://doi.org/10.1038/nphoton.2015.266\">10.1038/nphoton.2015.266</a>.","chicago":"Danzl, Johann G, Sven Sidenstein, Carola Gregor, Nicolai Urban, Peter Ilgen, Stefan Jakobs, and Stefan Hell. “Coordinate-Targeted Fluorescence Nanoscopy with Multiple off States.” <i>Nature Photonics</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nphoton.2015.266\">https://doi.org/10.1038/nphoton.2015.266</a>.","ista":"Danzl JG, Sidenstein S, Gregor C, Urban N, Ilgen P, Jakobs S, Hell S. 2016. Coordinate-targeted fluorescence nanoscopy with multiple off states. Nature Photonics. 10(2), 122–128.","ieee":"J. G. Danzl <i>et al.</i>, “Coordinate-targeted fluorescence nanoscopy with multiple off states,” <i>Nature Photonics</i>, vol. 10, no. 2. Nature Publishing Group, pp. 122–128, 2016.","short":"J.G. Danzl, S. Sidenstein, C. Gregor, N. Urban, P. Ilgen, S. Jakobs, S. Hell, Nature Photonics 10 (2016) 122–128.","ama":"Danzl JG, Sidenstein S, Gregor C, et al. Coordinate-targeted fluorescence nanoscopy with multiple off states. <i>Nature Photonics</i>. 2016;10(2):122-128. doi:<a href=\"https://doi.org/10.1038/nphoton.2015.266\">10.1038/nphoton.2015.266</a>"},"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank T. Gilat and E. Rothermel (both MPI) for help with preparing samples, and J. Keller for discussion. J.G.D. acknowledges support by the European Union through a Marie Curie fellowship PIEF-GA-2011-299283. S.W.H. acknowledges support by the Körber Foundation.","date_published":"2016-02-01T00:00:00Z","day":"01","article_processing_charge":"No","author":[{"first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"},{"last_name":"Sidenstein","full_name":"Sidenstein, Sven","first_name":"Sven"},{"full_name":"Gregor, Carola","last_name":"Gregor","first_name":"Carola"},{"first_name":"Nicolai","full_name":"Urban, Nicolai","last_name":"Urban"},{"first_name":"Peter","full_name":"Ilgen, Peter","last_name":"Ilgen"},{"first_name":"Stefan","last_name":"Jakobs","full_name":"Jakobs, Stefan"},{"first_name":"Stefan","last_name":"Hell","full_name":"Hell, Stefan"}],"doi":"10.1038/nphoton.2015.266","publisher":"Nature Publishing Group","oa_version":"None","title":"Coordinate-targeted fluorescence nanoscopy with multiple off states","_id":"1057","volume":10,"date_updated":"2021-01-12T06:47:58Z","date_created":"2018-12-11T11:49:55Z","type":"journal_article","page":"122 - 128","intvolume":"        10","abstract":[{"text":"Far-field super-resolution fluorescence microscopy discerns fluorophores residing closer than the diffraction barrier by briefly transferring them in different (typically ON and OFF) states before detection. In coordinate-targeted super-resolution variants, such as stimulated emission depletion (STED) microscopy, this state difference is created by the intensity minima and maxima of an optical pattern, causing all fluorophores to assume the off state, for instance, except at the minima. Although strong spatial confinement of the on state enables high resolution, it also subjects the fluorophores to excess intensities and state cycles at the maxima. Here, we address these issues by driving the fluorophores into a second off state that is inert to the excess light. By using reversibly switchable fluorescent proteins as labels, our approach reduces bleaching and enhances resolution and contrast in live-cell STED microscopy. Using two or more transitions to off states is a useful strategy for augmenting the power of coordinate-targeted super-resolution microscopy.","lang":"eng"}],"publication_status":"published"},{"year":"2016","month":"03","publist_id":"6330","status":"public","language":[{"iso":"eng"}],"extern":"1","publication":"Angewandte Chemie - International Edition","issue":"10","citation":{"mla":"Butkevich, Alexey, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 10, Wiley-Blackwell, 2016, pp. 3290–94, doi:<a href=\"https://doi.org/10.1002/anie.201511018\">10.1002/anie.201511018</a>.","apa":"Butkevich, A., Mitronova, G., Sidenstein, S., Klocke, J., Kamin, D., Meineke, D., … Hell, S. (2016). Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/anie.201511018\">https://doi.org/10.1002/anie.201511018</a>","ista":"Butkevich A, Mitronova G, Sidenstein S, Klocke J, Kamin D, Meineke D, D’Este E, Kraemer P, Danzl JG, Belov V, Hell S. 2016. Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. Angewandte Chemie - International Edition. 55(10), 3290–3294.","chicago":"Butkevich, Alexey, Gyuzel Mitronova, Sven Sidenstein, Jessica Klocke, Dirk Kamin, Dirk Meineke, Elisa D’Este, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1002/anie.201511018\">https://doi.org/10.1002/anie.201511018</a>.","short":"A. Butkevich, G. Mitronova, S. Sidenstein, J. Klocke, D. Kamin, D. Meineke, E. D’Este, P. Kraemer, J.G. Danzl, V. Belov, S. Hell, Angewandte Chemie - International Edition 55 (2016) 3290–3294.","ieee":"A. Butkevich <i>et al.</i>, “Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells,” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 10. Wiley-Blackwell, pp. 3290–3294, 2016.","ama":"Butkevich A, Mitronova G, Sidenstein S, et al. Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. <i>Angewandte Chemie - International Edition</i>. 2016;55(10):3290-3294. doi:<a href=\"https://doi.org/10.1002/anie.201511018\">10.1002/anie.201511018</a>"},"acknowledgement":"We thank Prof. Y. Okada (RIKEN Quantitative Biology Center, Osaka, Japan) for the gift of β-tubulin-Halo plasmid, T. Gilat and Dr. E. Rothermel (MPIBPC, Göttingen, Germany) for cell culture and transfection, M. Pulst, J. Bienert (MPIBPC), Dr. M. John, Dr. H. Frauendorf, and co-workers (Institut für Organische und Biomolekulare Chemie, Georg-August-Universität, Göttingen, Germany) for UV/Vis, NMR, and ESI-MS spectra, Prof. M. L. Bossi (University of Buenos-Aires, Argentina) for measuring fluorescence lifetimes, and Dr. S. Vos and Prof. P. Cramer (MPIBPC) for access to a Tecan microplate reader. S.W.H. acknowledges a grant from the Bundesministerium für Bildung und Forschung (BMBF 513) within the program “Optische Technologien für Biowissenschaften und Gesundheit” (FKZ 13N11066). J.G.D. was supported by funds from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013; REA grant agreement PIEF-GA-2011-299283).","date_published":"2016-03-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1002/anie.201511018","author":[{"full_name":"Butkevich, Alexey","last_name":"Butkevich","first_name":"Alexey"},{"first_name":"Gyuzel","last_name":"Mitronova","full_name":"Mitronova, Gyuzel"},{"first_name":"Sven","full_name":"Sidenstein, Sven","last_name":"Sidenstein"},{"full_name":"Klocke, Jessica","last_name":"Klocke","first_name":"Jessica"},{"last_name":"Kamin","full_name":"Kamin, Dirk","first_name":"Dirk"},{"full_name":"Meineke, Dirk","last_name":"Meineke","first_name":"Dirk"},{"first_name":"Elisa","last_name":"D'Este","full_name":"D'Este, Elisa"},{"full_name":"Kraemer, Philip","last_name":"Kraemer","first_name":"Philip"},{"last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973"},{"first_name":"Vladimir","full_name":"Belov, Vladimir","last_name":"Belov"},{"last_name":"Hell","full_name":"Hell, Stefan","first_name":"Stefan"}],"day":"01","article_processing_charge":"No","publisher":"Wiley-Blackwell","title":"Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells","oa_version":"None","date_updated":"2021-01-12T06:47:59Z","_id":"1059","volume":55,"type":"journal_article","date_created":"2018-12-11T11:49:55Z","page":"3290 - 3294","intvolume":"        55","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"abstract":[{"text":"A range of bright and photostable rhodamines and carbopyronines with absorption maxima in the range of λ=500-630 nm were prepared, and enabled the specific labeling of cytoskeletal filaments using HaloTag technology followed by staining with 1 μm solutions of the dye-ligand conjugates. The synthesis, photophysical parameters, fluorogenic behavior, and structure-property relationships of the new dyes are discussed. Light microscopy with stimulated emission depletion (STED) provided one- and two-color images of living cells with an optical resolution of 40-60 nm.","lang":"eng"}],"publication_status":"published"},{"publication_status":"published","abstract":[{"text":"Superresolution fluorescence microscopy of multiple fluorophores still requires development. Here we present simultaneous three-colour stimulated emission depletion (STED) nanoscopy relying on a single STED beam at 620 nm. Toggling the STED beam between two or more power levels (&quot;multilevelSTEDv) optimizes resolution and contrast in all colour channels, which are intrinsically co-aligned and well separated. Three-colour recording is demonstrated by imaging the nanoscale cytoskeletal organization in cultured hippocampal neurons. The down to ∼35 nm resolution identified periodic actin/betaII spectrin lattices along dendrites and spines; however, at presynaptic and postsynaptic sites, these patterns were found to be absent. Both our multicolour scheme and the 620 nm STED line should be attractive for routine STED microscopy applications.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"         6","page":"1 - 8","date_created":"2018-12-11T11:49:56Z","type":"journal_article","_id":"1060","volume":6,"date_updated":"2021-01-12T06:47:59Z","title":"Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses","oa_version":"None","publisher":"Nature Publishing Group","day":"25","article_processing_charge":"No","author":[{"first_name":"Sven","full_name":"Sidenstein, Sven","last_name":"Sidenstein"},{"first_name":"Elisa","full_name":"D'Este, Elisa","last_name":"D'Este"},{"first_name":"Marvin","full_name":"Böhm, Marvin","last_name":"Böhm"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973"},{"first_name":"Vladimir","last_name":"Belov","full_name":"Belov, Vladimir"},{"first_name":"Stefan","last_name":"Hell","full_name":"Hell, Stefan"}],"doi":"10.1038/srep26725","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2016-05-25T00:00:00Z","acknowledgement":"We acknowledge the assistance of I. Herfort with neuron preparation, and of J. Bienert and K. Müller with analyses of the dye 540R derivatives. We thank T. Gilat and E. Rothermel for sample preparation as well as J. Keller, F. Winter (all MPI-BPC) and C.A. Wurm (Abberior Instruments) for helpful discussion, and S.J. Sahl (MPI-BPC) for a critical reading of the manuscript.","citation":{"chicago":"Sidenstein, Sven, Elisa D’Este, Marvin Böhm, Johann G Danzl, Vladimir Belov, and Stefan Hell. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin Organization at Synapses.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep26725\">https://doi.org/10.1038/srep26725</a>.","ista":"Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. 2016. Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. Scientific Reports. 6, 1–8.","mla":"Sidenstein, Sven, et al. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin Organization at Synapses.” <i>Scientific Reports</i>, vol. 6, Nature Publishing Group, 2016, pp. 1–8, doi:<a href=\"https://doi.org/10.1038/srep26725\">10.1038/srep26725</a>.","apa":"Sidenstein, S., D’Este, E., Böhm, M., Danzl, J. G., Belov, V., &#38; Hell, S. (2016). Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep26725\">https://doi.org/10.1038/srep26725</a>","ama":"Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. <i>Scientific Reports</i>. 2016;6:1-8. doi:<a href=\"https://doi.org/10.1038/srep26725\">10.1038/srep26725</a>","short":"S. Sidenstein, E. D’Este, M. Böhm, J.G. Danzl, V. Belov, S. Hell, Scientific Reports 6 (2016) 1–8.","ieee":"S. Sidenstein, E. D’Este, M. Böhm, J. G. Danzl, V. Belov, and S. Hell, “Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, pp. 1–8, 2016."},"language":[{"iso":"eng"}],"publication":"Scientific Reports","extern":"1","status":"public","publist_id":"6329","month":"05","year":"2016"},{"year":"2016","month":"11","department":[{"_id":"SiHi"}],"publist_id":"6172","project":[{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425"}],"status":"public","language":[{"iso":"eng"}],"publication":"Journal of Neuroscience","issue":"45","citation":{"short":"N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, T. Ghashghaei, Journal of Neuroscience 36 (2016) 11394–11401.","ieee":"N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, and T. Ghashghaei, “Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity,” <i>Journal of Neuroscience</i>, vol. 36, no. 45. Society for Neuroscience, pp. 11394–11401, 2016.","ama":"Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. <i>Journal of Neuroscience</i>. 2016;36(45):11394-11401. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">10.1523/JNEUROSCI.2359-16.2016</a>","mla":"Dwyer, Noelle, et al. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity.” <i>Journal of Neuroscience</i>, vol. 36, no. 45, Society for Neuroscience, 2016, pp. 11394–401, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">10.1523/JNEUROSCI.2359-16.2016</a>.","apa":"Dwyer, N., Chen, B., Chou, S., Hippenmeyer, S., Nguyen, L., &#38; Ghashghaei, T. (2016). Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">https://doi.org/10.1523/JNEUROSCI.2359-16.2016</a>","chicago":"Dwyer, Noelle, Bin Chen, Shen Chou, Simon Hippenmeyer, Laurent Nguyen, and Troy Ghashghaei. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2016. <a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">https://doi.org/10.1523/JNEUROSCI.2359-16.2016</a>.","ista":"Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. 2016. Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. Journal of Neuroscience. 36(45), 11394–11401."},"date_published":"2016-11-09T00:00:00Z","acknowledgement":"This work was supported by National Institutes of Health Grants R01NS089795 and R01NS098370 to H.T.G., R01NS076640 to N.D.D., and R01MH094589 and R01NS089777 to B.C., Academia Sinica AS-104-TPB09-2 to S.-J.C, European Union FP7-CIG618444 and Human Frontiers Science Program RGP0053 to S.H., and Fonds Léon Fredericq, from the Fondation Médicale Reine Elisabeth, and from the Fonation Simone et Pierre Clerdent to L.N. The authors apologize to colleagues whose work could not be cited due to space limitations.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1523/JNEUROSCI.2359-16.2016","author":[{"first_name":"Noelle","last_name":"Dwyer","full_name":"Dwyer, Noelle"},{"first_name":"Bin","last_name":"Chen","full_name":"Chen, Bin"},{"first_name":"Shen","last_name":"Chou","full_name":"Chou, Shen"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"first_name":"Laurent","full_name":"Nguyen, Laurent","last_name":"Nguyen"},{"full_name":"Ghashghaei, Troy","last_name":"Ghashghaei","first_name":"Troy"}],"scopus_import":1,"day":"09","title":"Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity","oa_version":"None","publisher":"Society for Neuroscience","date_updated":"2021-01-12T06:48:54Z","volume":36,"_id":"1181","type":"journal_article","date_created":"2018-12-11T11:50:35Z","page":"11394 - 11401","intvolume":"        36","abstract":[{"lang":"eng","text":"This review accompanies a 2016 SFN mini-symposium presenting examples of current studies that address a central question: How do neural stem cells (NSCs) divide in different ways to produce heterogeneous daughter types at the right time and in proper numbers to build a cerebral cortex with the appropriate size and structure? We will focus on four aspects of corticogenesis: cytokinesis events that follow apical mitoses of NSCs; coordinating abscission with delamination from the apical membrane; timing of neurogenesis and its indirect regulation through emergence of intermediate progenitors; and capacity of single NSCs to generate the correct number and laminar fate of cortical neurons. Defects in these mechanisms can cause microcephaly and other brain malformations, and understanding them is critical to designing diagnostic tools and preventive and corrective therapies."}],"quality_controlled":"1","publication_status":"published"},{"publisher":"AAAI Press","oa_version":"Preprint","title":"Robust draws in balanced knockout tournaments","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"},{"first_name":"Josef","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec"}],"scopus_import":1,"day":"01","type":"conference","date_created":"2018-12-11T11:50:35Z","date_updated":"2023-02-21T10:04:26Z","_id":"1182","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"}],"page":"172 - 179","publication_status":"published","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.05090v1"}],"month":"01","related_material":{"link":[{"url":"https://www.ijcai.org/proceedings/2016","relation":"table_of_contents"}]},"year":"2016","publist_id":"6171","department":[{"_id":"KrCh"}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"status":"public","language":[{"iso":"eng"}],"oa":1,"date_published":"2016-01-01T00:00:00Z","conference":{"location":"New York, NY, USA","name":"IJCAI: International Joint Conference on Artificial Intelligence","end_date":"2016-07-15","start_date":"2016-07-09"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"citation":{"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.","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.","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.","ama":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179."}},{"publication_status":"published","file_date_updated":"2020-07-14T12:44:37Z","has_accepted_license":"1","intvolume":"       167","abstract":[{"lang":"eng","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."}],"volume":167,"article_type":"original","date_created":"2018-12-11T11:50:35Z","author":[{"full_name":"Tarlungeanu, Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","last_name":"Tarlungeanu","first_name":"Dora-Clara"},{"first_name":"Elena","orcid":"0000-0002-7370-5293","full_name":"Deliu, Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","last_name":"Deliu"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","last_name":"Dotter","orcid":"0000-0002-9033-9096","first_name":"Christoph"},{"full_name":"Kara, Majdi","last_name":"Kara","first_name":"Majdi"},{"first_name":"Philipp","last_name":"Janiesch","full_name":"Janiesch, Philipp"},{"last_name":"Scalise","full_name":"Scalise, Mariafrancesca","first_name":"Mariafrancesca"},{"full_name":"Galluccio, Michele","last_name":"Galluccio","first_name":"Michele"},{"full_name":"Tesulov, Mateja","last_name":"Tesulov","first_name":"Mateja"},{"first_name":"Emanuela","last_name":"Morelli","id":"3F4D1282-F248-11E8-B48F-1D18A9856A87","full_name":"Morelli, Emanuela"},{"full_name":"Sönmez, Fatma","last_name":"Sönmez","first_name":"Fatma"},{"first_name":"Kaya","last_name":"Bilgüvar","full_name":"Bilgüvar, Kaya"},{"full_name":"Ohgaki, Ryuichi","last_name":"Ohgaki","first_name":"Ryuichi"},{"first_name":"Yoshikatsu","last_name":"Kanai","full_name":"Kanai, Yoshikatsu"},{"first_name":"Anide","full_name":"Johansen, Anide","last_name":"Johansen"},{"last_name":"Esharif","full_name":"Esharif, Seham","first_name":"Seham"},{"first_name":"Tawfeg","last_name":"Ben Omran","full_name":"Ben Omran, Tawfeg"},{"full_name":"Topcu, Meral","last_name":"Topcu","first_name":"Meral"},{"first_name":"Avner","full_name":"Schlessinger, Avner","last_name":"Schlessinger"},{"full_name":"Indiveri, Cesare","last_name":"Indiveri","first_name":"Cesare"},{"first_name":"Kent","full_name":"Duncan, Kent","last_name":"Duncan"},{"first_name":"Ahmet","last_name":"Caglayan","full_name":"Caglayan, Ahmet"},{"last_name":"Günel","full_name":"Günel, Murat","first_name":"Murat"},{"first_name":"Joseph","full_name":"Gleeson, Joseph","last_name":"Gleeson"},{"orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino"}],"day":"01","scopus_import":"1","title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","oa_version":"Submitted Version","issue":"6","citation":{"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.","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.","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>","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>.","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>","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>."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"pubrep_id":"771","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"file":[{"file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7fe01ab12a6610d3db421e0136db2f77","date_created":"2018-12-12T10:13:44Z","file_size":73907957,"date_updated":"2020-07-14T12:44:37Z","creator":"system","file_id":"5030"}],"month":"12","quality_controlled":"1","page":"1481 - 1494","ddc":["576","616"],"date_updated":"2024-03-25T23:30:07Z","_id":"1183","type":"journal_article","doi":"10.1016/j.cell.2016.11.013","article_processing_charge":"No","publisher":"Cell Press","date_published":"2016-12-01T00:00:00Z","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","project":[{"_id":"25473368-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Transmembrane Transporters in Health and Disease","grant_number":"F03523"}],"publication":"Cell","status":"public","publist_id":"6170","year":"2016","related_material":{"record":[{"id":"395","status":"public","relation":"dissertation_contains"}]}},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPIcs.ESA.2016.46"}],"quality_controlled":"1","_id":"11834","date_updated":"2023-02-16T12:05:59Z","type":"conference","article_processing_charge":"No","alternative_title":["LIPIcs"],"doi":"10.4230/LIPICS.ESA.2016.46","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"location":"Aarhus, Denmark","end_date":"2016-08-24","start_date":"2016-08-22","name":"ESA: Annual European Symposium on Algorithms"},"date_published":"2016-08-18T00:00:00Z","status":"public","extern":"1","publication":"24th Annual European Symposium on Algorithms","year":"2016","external_id":{"arxiv":["1611.06500"]},"publication_status":"published","publication_identifier":{"isbn":["978-3-95977-015-6"],"issn":["1868-8969"]},"abstract":[{"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.","lang":"eng"}],"intvolume":"        57","volume":57,"date_created":"2022-08-12T10:58:32Z","day":"18","scopus_import":"1","author":[{"full_name":"Goranci, Gramoz","last_name":"Goranci","first_name":"Gramoz"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","first_name":"Monika H","orcid":"0000-0002-5008-6530"},{"last_name":"Thorup","full_name":"Thorup, Mikkel","first_name":"Mikkel"}],"oa_version":"Published Version","title":"Incremental exact min-cut in poly-logarithmic amortized update time","citation":{"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>.","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>","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.","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.","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>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"article_number":"46","arxiv":1,"month":"08"},{"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPIcs.ESA.2016.48"}],"type":"conference","date_updated":"2023-02-16T12:07:46Z","_id":"11835","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","doi":"10.4230/LIPICS.ESA.2016.48","alternative_title":["LIPIcs"],"article_processing_charge":"No","date_published":"2016-08-18T00:00:00Z","conference":{"location":"Aarhus, Denmark","start_date":"2016-08-22","end_date":"2016-08-24","name":"ESA: Annual European Symposium on Algorithms"},"publication":"24th Annual European Symposium on Algorithms","extern":"1","status":"public","external_id":{"arxiv":["1611.05248"]},"year":"2016","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-015-6"]},"publication_status":"published","intvolume":"        57","abstract":[{"lang":"eng","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."}],"date_created":"2022-08-12T11:05:41Z","volume":57,"title":"Incremental and fully dynamic subgraph connectivity for emergency planning","oa_version":"Published Version","author":[{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","first_name":"Monika H","orcid":"0000-0002-5008-6530"},{"last_name":"Neumann","full_name":"Neumann, Stefan","first_name":"Stefan"}],"day":"18","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>.","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.","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.","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>"},"language":[{"iso":"eng"}],"oa":1,"article_number":"48","arxiv":1,"month":"08"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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>","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>","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."},"language":[{"iso":"eng"}],"oa":1,"article_number":"131","arxiv":1,"month":"08","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-013-2"]},"publication_status":"published","intvolume":"        55","abstract":[{"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.","lang":"eng"}],"date_created":"2022-08-12T11:16:01Z","volume":55,"oa_version":"Published Version","title":"Graph minors for preserving terminal distances approximately - lower and upper bounds","scopus_import":"1","day":"23","author":[{"full_name":"Cheung, Yun Kuen","last_name":"Cheung","first_name":"Yun Kuen"},{"first_name":"Gramoz","last_name":"Goranci","full_name":"Goranci, Gramoz"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"}],"date_published":"2016-08-23T00:00:00Z","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","end_date":"2016-07-15","start_date":"2016-07-12","location":"Rome, Italy"},"extern":"1","publication":"43rd International Colloquium on Automata, Languages, and Programming","status":"public","external_id":{"arxiv":["1604.08342"]},"year":"2016","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.4230/LIPICS.ICALP.2016.131","open_access":"1"}],"type":"conference","_id":"11836","date_updated":"2023-02-16T12:09:54Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_processing_charge":"No","alternative_title":["LIPIcs"],"doi":"10.4230/LIPICS.ICALP.2016.131"},{"publication_status":"published","file_date_updated":"2020-07-14T12:44:37Z","intvolume":"         6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"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."}],"has_accepted_license":"1","date_created":"2018-12-11T11:50:36Z","volume":6,"title":"Mating and longevity in ant males","oa_version":"Published Version","author":[{"full_name":"Metzler, Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","last_name":"Metzler","first_name":"Sina"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"first_name":"Alexandra","full_name":"Schrempf, Alexandra","last_name":"Schrempf"}],"day":"01","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"24","citation":{"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>.","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>","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>.","short":"S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906.","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.","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>"},"pubrep_id":"736","language":[{"iso":"eng"}],"oa":1,"file":[{"file_id":"5062","creator":"system","date_updated":"2020-07-14T12:44:37Z","file_size":328414,"date_created":"2018-12-12T10:14:12Z","checksum":"789026eb9e1be2a0da08376f29f569cf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf"}],"department":[{"_id":"SyCr"}],"month":"12","quality_controlled":"1","ddc":["576","592"],"page":"8903 - 8906","type":"journal_article","date_updated":"2021-01-12T06:48:55Z","_id":"1184","publisher":"Wiley-Blackwell","doi":"10.1002/ece3.2474","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.","date_published":"2016-12-01T00:00:00Z","status":"public","publication":"Ecology and Evolution","publist_id":"6169","year":"2016"},{"acknowledgement":"M.C. was funded by a PhD fellowship from the Università degli Studi di Milano-Bicocca and from Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR) [MIUR-PRIN 2012]. L.C. is also supported by MIUR [MIUR-PRIN 2012]. We would like to thank Andrew MacCabe and Edward Kiegle for editing the paper.","date_published":"2016-12-01T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"23","citation":{"apa":"Cucinotta, M., Manrique, S., Guazzotti, A., Quadrelli, N., Mendes, M., Benková, E., &#38; Colombo, L. (2016). Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.143545\">https://doi.org/10.1242/dev.143545</a>","mla":"Cucinotta, Mara, et al. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” <i>Development</i>, vol. 143, no. 23, Company of Biologists, 2016, pp. 4419–24, doi:<a href=\"https://doi.org/10.1242/dev.143545\">10.1242/dev.143545</a>.","chicago":"Cucinotta, Mara, Silvia Manrique, Andrea Guazzotti, Nadia Quadrelli, Marta Mendes, Eva Benková, and Lucia Colombo. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” <i>Development</i>. Company of Biologists, 2016. <a href=\"https://doi.org/10.1242/dev.143545\">https://doi.org/10.1242/dev.143545</a>.","ista":"Cucinotta M, Manrique S, Guazzotti A, Quadrelli N, Mendes M, Benková E, Colombo L. 2016. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. 143(23), 4419–4424.","ieee":"M. Cucinotta <i>et al.</i>, “Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development,” <i>Development</i>, vol. 143, no. 23. Company of Biologists, pp. 4419–4424, 2016.","short":"M. Cucinotta, S. Manrique, A. Guazzotti, N. Quadrelli, M. Mendes, E. Benková, L. Colombo, Development 143 (2016) 4419–4424.","ama":"Cucinotta M, Manrique S, Guazzotti A, et al. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. <i>Development</i>. 2016;143(23):4419-4424. doi:<a href=\"https://doi.org/10.1242/dev.143545\">10.1242/dev.143545</a>"},"status":"public","language":[{"iso":"eng"}],"publication":"Development","publist_id":"6168","department":[{"_id":"EvBe"}],"month":"12","year":"2016","publication_status":"published","quality_controlled":"1","abstract":[{"lang":"eng","text":"The developmental programme of the pistil is under the control of both auxin and cytokinin. Crosstalk between these factors converges on regulation of the auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length and ovule number were reduced. PIN1 expression was also lower in the triple mutant and the phenotypes could not be rescued by exogenous cytokinin application. pin1 complementation studies using genomic PIN1 constructs showed that the pistil phenotypes were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating the pivotal role of CRFs in auxin-cytokinin crosstalk."}],"intvolume":"       143","page":"4419 - 4424","type":"journal_article","date_created":"2018-12-11T11:50:36Z","date_updated":"2021-01-12T06:48:56Z","_id":"1185","volume":143,"title":"Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development","oa_version":"None","publisher":"Company of Biologists","author":[{"first_name":"Mara","last_name":"Cucinotta","full_name":"Cucinotta, Mara"},{"first_name":"Silvia","full_name":"Manrique, Silvia","last_name":"Manrique"},{"first_name":"Andrea","full_name":"Guazzotti, Andrea","last_name":"Guazzotti"},{"full_name":"Quadrelli, Nadia","last_name":"Quadrelli","first_name":"Nadia"},{"full_name":"Mendes, Marta","last_name":"Mendes","first_name":"Marta"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva"},{"last_name":"Colombo","full_name":"Colombo, Lucia","first_name":"Lucia"}],"doi":"10.1242/dev.143545","scopus_import":1,"day":"01"},{"quality_controlled":"1","ddc":["576","610"],"type":"journal_article","_id":"1186","date_updated":"2021-01-12T06:48:56Z","publisher":"Nature Publishing Group","doi":"10.1038/srep38094","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).","date_published":"2016-12-05T00:00:00Z","publication":"Scientific Reports","status":"public","publist_id":"6167","year":"2016","file_date_updated":"2020-07-14T12:44:37Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"         6","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"}],"has_accepted_license":"1","date_created":"2018-12-11T11:50:36Z","volume":6,"title":"Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis","oa_version":"Published Version","scopus_import":1,"day":"05","author":[{"first_name":"Javier","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","full_name":"Gutierrez-Fernandez, Javier","last_name":"Gutierrez-Fernandez"},{"first_name":"Malek","last_name":"Saleh","full_name":"Saleh, Malek"},{"first_name":"Martín","full_name":"Alcorlo, Martín","last_name":"Alcorlo"},{"first_name":"Alejandro","full_name":"Gómez Mejóa, Alejandro","last_name":"Gómez Mejóa"},{"last_name":"Pantoja Uceda","full_name":"Pantoja Uceda, David","first_name":"David"},{"full_name":"Treviño, Miguel","last_name":"Treviño","first_name":"Miguel"},{"first_name":"Franziska","full_name":"Vob, Franziska","last_name":"Vob"},{"last_name":"Abdullah","full_name":"Abdullah, Mohammed","first_name":"Mohammed"},{"last_name":"Galán Bartual","full_name":"Galán Bartual, Sergio","first_name":"Sergio"},{"full_name":"Seinen, Jolien","last_name":"Seinen","first_name":"Jolien"},{"first_name":"Pedro","last_name":"Sánchez Murcia","full_name":"Sánchez Murcia, Pedro"},{"first_name":"Federico","full_name":"Gago, Federico","last_name":"Gago"},{"full_name":"Bruix, Marta","last_name":"Bruix","first_name":"Marta"},{"first_name":"Sven","full_name":"Hammerschmidt, Sven","last_name":"Hammerschmidt"},{"first_name":"Juan","last_name":"Hermoso","full_name":"Hermoso, Juan"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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>","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>.","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.","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.","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).","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>"},"pubrep_id":"735","language":[{"iso":"eng"}],"oa":1,"file":[{"file_size":2716045,"date_created":"2018-12-12T10:10:18Z","creator":"system","date_updated":"2020-07-14T12:44:37Z","file_id":"4804","file_name":"IST-2017-735-v1+1_srep38094.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e007d78b483bc59bf5ab98e9d42a6ec1"}],"article_number":"38094","department":[{"_id":"LeSa"}],"month":"12"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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>","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>.","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."},"language":[{"iso":"eng"}],"oa":1,"arxiv":1,"month":"06","publication_status":"published","publication_identifier":{"isbn":["978-145034132-5"],"issn":["0737-8017"]},"abstract":[{"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].","lang":"eng"}],"date_created":"2022-08-16T09:19:31Z","title":"A deterministic almost-tight distributed algorithm for approximating single-source shortest paths","oa_version":"Preprint","author":[{"orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"},{"first_name":"Sebastian","full_name":"Krinninger, Sebastian","last_name":"Krinninger"},{"full_name":"Nanongkai, Danupon","last_name":"Nanongkai","first_name":"Danupon"}],"day":"01","scopus_import":"1","conference":{"location":"Cambridge, MA, United States","start_date":"2016-06-19","end_date":"2016-06-21","name":"STOC: Symposium on Theory of Computing"},"date_published":"2016-06-01T00:00:00Z","publication":"48th Annual ACM SIGACT Symposium on Theory of Computing","status":"public","extern":"1","external_id":{"arxiv":["1504.07056"]},"year":"2016","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.07056"}],"page":"489 - 498","type":"conference","date_updated":"2023-02-17T10:32:23Z","_id":"11866","publisher":"Association for Computing Machinery","doi":"10.1145/2897518.2897638","article_processing_charge":"No"},{"_id":"11867","date_updated":"2023-02-17T11:08:19Z","type":"conference","article_processing_charge":"No","doi":"10.1145/2897518.2897568","publisher":"Association for Computing Machinery","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.05765"}],"quality_controlled":"1","page":"398 - 411","year":"2016","external_id":{"arxiv":["1604.05765"]},"conference":{"end_date":"2016-06-21","start_date":"2016-06-19","name":"STOC: Symposium on Theory of Computing","location":"Cambridge, MA, United States"},"date_published":"2016-06-01T00:00:00Z","status":"public","publication":"48th Annual ACM SIGACT Symposium on Theory of Computing","extern":"1","date_created":"2022-08-16T09:27:35Z","day":"01","scopus_import":"1","author":[{"last_name":"Bhattacharya","full_name":"Bhattacharya, Sayan","first_name":"Sayan"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"}],"oa_version":"Preprint","title":"New deterministic approximation algorithms for fully dynamic matching","publication_status":"published","publication_identifier":{"issn":["0737-8017"],"isbn":["978-145034132-5"]},"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."}],"arxiv":1,"month":"06","citation":{"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>.","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>","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>.","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.","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>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}]},{"article_number":"123502","department":[{"_id":"GaTk"}],"month":"12","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"12","citation":{"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>","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.","short":"D. De Martino, D. Masoero,  Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).","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>.","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.","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>","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>."},"language":[{"iso":"eng"}],"oa":1,"date_created":"2018-12-11T11:50:37Z","volume":2016,"title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth","oa_version":"Preprint","author":[{"first_name":"Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele"},{"first_name":"Davide","last_name":"Masoero","full_name":"Masoero, Davide"}],"day":"30","scopus_import":1,"publication_status":"published","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."}],"intvolume":"      2016","publist_id":"6165","year":"2016","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.","date_published":"2016-12-30T00:00:00Z","ec_funded":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"publication":" Journal of Statistical Mechanics: Theory and Experiment","status":"public","type":"journal_article","date_updated":"2021-01-12T06:48:57Z","_id":"1188","publisher":"IOPscience","doi":"10.1088/1742-5468/aa4e8f","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.09048"}]}]