[{"article_number":"224102","arxiv":1,"title":"Non-equilibrium simulations of thermally induced electric fields in water","author":[{"first_name":"P.","last_name":"Wirnsberger","full_name":"Wirnsberger, P."},{"first_name":"D.","last_name":"Fijan","full_name":"Fijan, D."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Neumann, M.","last_name":"Neumann","first_name":"M."},{"last_name":"Dellago","first_name":"C.","full_name":"Dellago, C."},{"first_name":"D.","last_name":"Frenkel","full_name":"Frenkel, D."}],"day":"10","publication":"The Journal of Chemical Physics","article_type":"original","article_processing_charge":"No","scopus_import":"1","publisher":"American Institute of Physics","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","pmid":1,"doi":"10.1063/1.4953036","quality_controlled":"1","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"keyword":["physical and theoretical chemistry","general physics and astronomy"],"issue":"22","language":[{"iso":"eng"}],"volume":144,"date_created":"2021-11-29T11:08:52Z","type":"journal_article","month":"06","oa_version":"Preprint","date_updated":"2021-11-29T13:09:08Z","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"}],"_id":"10380","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).","year":"2016","date_published":"2016-06-10T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02734"}],"publication_status":"published","oa":1,"extern":"1","intvolume":" 144","citation":{"chicago":"Wirnsberger, P., D. Fijan, Anđela Šarić, M. Neumann, C. Dellago, and D. Frenkel. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” The Journal of Chemical Physics. American Institute of Physics, 2016. https://doi.org/10.1063/1.4953036.","ieee":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, and D. Frenkel, “Non-equilibrium simulations of thermally induced electric fields in water,” The Journal of Chemical Physics, vol. 144, no. 22. American Institute of Physics, 2016.","short":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The Journal of Chemical Physics 144 (2016).","ama":"Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium simulations of thermally induced electric fields in water. The Journal of Chemical Physics. 2016;144(22). doi:10.1063/1.4953036","apa":"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. American Institute of Physics. https://doi.org/10.1063/1.4953036","mla":"Wirnsberger, P., et al. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” The Journal of Chemical Physics, vol. 144, no. 22, 224102, American Institute of Physics, 2016, doi:10.1063/1.4953036.","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."},"status":"public","external_id":{"pmid":["27305991"],"arxiv":["1602.02734"]}},{"status":"public","external_id":{"arxiv":["1608.05788"],"pmid":["27722701"]},"extern":"1","intvolume":" 12","citation":{"ama":"Bachmann SJ, Kotar J, Parolini L, et al. Melting transition in lipid vesicles functionalised by mobile DNA linkers. Soft Matter. 2016;12(37):7804-7817. doi:10.1039/c6sm01515h","apa":"Bachmann, S. J., Kotar, J., Parolini, L., Šarić, A., Cicuta, P., Di Michele, L., & Mognetti, B. M. (2016). Melting transition in lipid vesicles functionalised by mobile DNA linkers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c6sm01515h","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.","mla":"Bachmann, Stephan Jan, et al. “Melting Transition in Lipid Vesicles Functionalised by Mobile DNA Linkers.” Soft Matter, vol. 12, no. 37, Royal Society of Chemistry, 2016, pp. 7804–17, doi:10.1039/c6sm01515h.","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.” Soft Matter. Royal Society of Chemistry, 2016. https://doi.org/10.1039/c6sm01515h.","ieee":"S. J. Bachmann et al., “Melting transition in lipid vesicles functionalised by mobile DNA linkers,” Soft Matter, vol. 12, no. 37. Royal Society of Chemistry, pp. 7804–7817, 2016.","short":"S.J. Bachmann, J. Kotar, L. Parolini, A. Šarić, P. Cicuta, L. Di Michele, B.M. Mognetti, Soft Matter 12 (2016) 7804–7817."},"oa":1,"publication_status":"published","date_published":"2016-08-19T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1608.05788","open_access":"1"}],"year":"2016","_id":"10381","page":"7804-7817","type":"journal_article","month":"08","oa_version":"Preprint","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."}],"date_updated":"2021-11-29T13:09:00Z","volume":12,"date_created":"2021-11-29T11:09:55Z","keyword":["condensed matter physics","general chemistry"],"issue":"37","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"doi":"10.1039/c6sm01515h","quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Royal Society of Chemistry","pmid":1,"publication":"Soft Matter","article_type":"original","article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Bachmann","first_name":"Stephan Jan","full_name":"Bachmann, Stephan Jan"},{"full_name":"Kotar, Jurij","first_name":"Jurij","last_name":"Kotar"},{"first_name":"Lucia","last_name":"Parolini","full_name":"Parolini, Lucia"},{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Cicuta, Pietro","first_name":"Pietro","last_name":"Cicuta"},{"first_name":"Lorenzo","last_name":"Di Michele","full_name":"Di Michele, Lorenzo"},{"full_name":"Mognetti, Bortolo Matteo","last_name":"Mognetti","first_name":"Bortolo Matteo"}],"day":"19","title":"Melting transition in lipid vesicles functionalised by mobile DNA linkers","arxiv":1},{"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"}],"status":"public","conference":{"end_date":"2016-07-15","location":"New York, NY, USA","name":"IJCAI: International Joint Conference on Artificial Intelligence","start_date":"2016-07-09"},"related_material":{"link":[{"relation":"table_of_contents","url":"https://www.ijcai.org/proceedings/2016"}]},"language":[{"iso":"eng"}],"citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179.","ista":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. 2016. Robust draws in balanced knockout tournaments. IJCAI: International Joint Conference on Artificial Intelligence vol. 2016–January, 172–179.","mla":"Chatterjee, Krishnendu, et al. Robust Draws in Balanced Knockout Tournaments. Vol. 2016–January, AAAI Press, 2016, pp. 172–79.","apa":"Chatterjee, K., Ibsen-Jensen, R., & 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.","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.","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."},"oa":1,"publication_status":"published","date_published":"2016-01-01T00:00:00Z","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1604.05090v1","open_access":"1"}],"publisher":"AAAI Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016","department":[{"_id":"KrCh"}],"_id":"1182","scopus_import":1,"ec_funded":1,"page":"172 - 179","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"}],"oa_version":"Preprint","type":"conference","month":"01","date_updated":"2023-02-21T10:04:26Z","abstract":[{"lang":"eng","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."}],"day":"01","volume":"2016-January","title":"Robust draws in balanced knockout tournaments","publist_id":"6171","date_created":"2018-12-11T11:50:35Z"},{"language":[{"iso":"eng"}],"issue":"6","project":[{"name":"Transmembrane Transporters in Health and Disease","_id":"25473368-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"F03523"}],"quality_controlled":"1","doi":"10.1016/j.cell.2016.11.013","pubrep_id":"771","article_processing_charge":"No","scopus_import":"1","article_type":"original","publication":"Cell","department":[{"_id":"GaNo"}],"publisher":"Cell Press","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publist_id":"6170","title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","file":[{"creator":"system","relation":"main_file","content_type":"application/pdf","file_size":73907957,"file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","access_level":"open_access","date_created":"2018-12-12T10:13:44Z","checksum":"7fe01ab12a6610d3db421e0136db2f77","date_updated":"2020-07-14T12:44:37Z","file_id":"5030"}],"day":"01","author":[{"first_name":"Dora-Clara","last_name":"Tarlungeanu","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","full_name":"Tarlungeanu, Dora-Clara"},{"last_name":"Deliu","first_name":"Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5293","full_name":"Deliu, Elena"},{"last_name":"Dotter","first_name":"Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph"},{"last_name":"Kara","first_name":"Majdi","full_name":"Kara, Majdi"},{"first_name":"Philipp","last_name":"Janiesch","full_name":"Janiesch, Philipp"},{"full_name":"Scalise, Mariafrancesca","last_name":"Scalise","first_name":"Mariafrancesca"},{"last_name":"Galluccio","first_name":"Michele","full_name":"Galluccio, Michele"},{"last_name":"Tesulov","first_name":"Mateja","full_name":"Tesulov, Mateja"},{"first_name":"Emanuela","last_name":"Morelli","full_name":"Morelli, Emanuela","id":"3F4D1282-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sönmez, Fatma","last_name":"Sönmez","first_name":"Fatma"},{"full_name":"Bilgüvar, Kaya","first_name":"Kaya","last_name":"Bilgüvar"},{"full_name":"Ohgaki, Ryuichi","first_name":"Ryuichi","last_name":"Ohgaki"},{"full_name":"Kanai, Yoshikatsu","last_name":"Kanai","first_name":"Yoshikatsu"},{"first_name":"Anide","last_name":"Johansen","full_name":"Johansen, Anide"},{"full_name":"Esharif, Seham","last_name":"Esharif","first_name":"Seham"},{"full_name":"Ben Omran, Tawfeg","last_name":"Ben Omran","first_name":"Tawfeg"},{"full_name":"Topcu, Meral","last_name":"Topcu","first_name":"Meral"},{"full_name":"Schlessinger, Avner","last_name":"Schlessinger","first_name":"Avner"},{"full_name":"Indiveri, Cesare","first_name":"Cesare","last_name":"Indiveri"},{"full_name":"Duncan, Kent","first_name":"Kent","last_name":"Duncan"},{"full_name":"Caglayan, Ahmet","first_name":"Ahmet","last_name":"Caglayan"},{"full_name":"Günel, Murat","last_name":"Günel","first_name":"Murat"},{"full_name":"Gleeson, Joseph","last_name":"Gleeson","first_name":"Joseph"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"}],"citation":{"mla":"Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell, vol. 167, no. 6, Cell Press, 2016, pp. 1481–94, doi:10.1016/j.cell.2016.11.013.","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.","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. Cell. Cell Press. https://doi.org/10.1016/j.cell.2016.11.013","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. Cell. 2016;167(6):1481-1494. doi:10.1016/j.cell.2016.11.013","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 et al., “Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder,” Cell, vol. 167, no. 6. Cell Press, pp. 1481–1494, 2016.","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.” Cell. Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.013."},"intvolume":" 167","related_material":{"record":[{"status":"public","id":"395","relation":"dissertation_contains"}]},"status":"public","date_published":"2016-12-01T00:00:00Z","ddc":["576","616"],"has_accepted_license":"1","publication_status":"published","oa":1,"_id":"1183","year":"2016","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","date_created":"2018-12-11T11:50:35Z","file_date_updated":"2020-07-14T12:44:37Z","volume":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."}],"date_updated":"2024-03-25T23:30:07Z","oa_version":"Submitted Version","month":"12","type":"journal_article","page":"1481 - 1494"},{"volume":57,"date_created":"2022-08-12T10:58:32Z","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"}],"date_updated":"2023-02-16T12:05:59Z","month":"08","oa_version":"Published Version","type":"conference","_id":"11834","year":"2016","date_published":"2016-08-18T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPIcs.ESA.2016.46"}],"oa":1,"publication_status":"published","extern":"1","intvolume":" 57","citation":{"ieee":"G. Goranci, M. H. Henzinger, and M. Thorup, “Incremental exact min-cut in poly-logarithmic amortized update time,” in 24th Annual European Symposium on Algorithms, Aarhus, Denmark, 2016, vol. 57.","chicago":"Goranci, Gramoz, Monika H Henzinger, and Mikkel Thorup. “Incremental Exact Min-Cut in Poly-Logarithmic Amortized Update Time.” In 24th Annual European Symposium on Algorithms, Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPICS.ESA.2016.46.","short":"G. Goranci, M.H. Henzinger, M. Thorup, in:, 24th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ama":"Goranci G, Henzinger MH, Thorup M. Incremental exact min-cut in poly-logarithmic amortized update time. In: 24th Annual European Symposium on Algorithms. Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPICS.ESA.2016.46","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.","mla":"Goranci, Gramoz, et al. “Incremental Exact Min-Cut in Poly-Logarithmic Amortized Update Time.” 24th Annual European Symposium on Algorithms, vol. 57, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPICS.ESA.2016.46.","apa":"Goranci, G., Henzinger, M. H., & Thorup, M. (2016). Incremental exact min-cut in poly-logarithmic amortized update time. In 24th Annual European Symposium on Algorithms (Vol. 57). Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2016.46"},"alternative_title":["LIPIcs"],"external_id":{"arxiv":["1611.06500"]},"status":"public","title":"Incremental exact min-cut in poly-logarithmic amortized update time","arxiv":1,"article_number":"46","author":[{"full_name":"Goranci, Gramoz","first_name":"Gramoz","last_name":"Goranci"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Thorup, Mikkel","first_name":"Mikkel","last_name":"Thorup"}],"day":"18","publication":"24th Annual European Symposium on Algorithms","article_processing_charge":"No","scopus_import":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.4230/LIPICS.ESA.2016.46","quality_controlled":"1","publication_identifier":{"isbn":["978-3-95977-015-6"],"issn":["1868-8969"]},"conference":{"end_date":"2016-08-24","start_date":"2016-08-22","location":"Aarhus, Denmark","name":"ESA: Annual European Symposium on Algorithms"},"language":[{"iso":"eng"}]},{"article_number":"48","title":"Incremental and fully dynamic subgraph connectivity for emergency planning","arxiv":1,"day":"18","author":[{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger"},{"last_name":"Neumann","first_name":"Stefan","full_name":"Neumann, Stefan"}],"scopus_import":"1","article_processing_charge":"No","publication":"24th Annual European Symposium on Algorithms","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","doi":"10.4230/LIPICS.ESA.2016.48","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-015-6"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2016-08-24","start_date":"2016-08-22","location":"Aarhus, Denmark","name":"ESA: Annual European Symposium on Algorithms"},"date_created":"2022-08-12T11:05:41Z","volume":57,"oa_version":"Published Version","month":"08","type":"conference","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_updated":"2023-02-16T12:07:46Z","_id":"11835","year":"2016","main_file_link":[{"url":"https://doi.org/10.4230/LIPIcs.ESA.2016.48","open_access":"1"}],"date_published":"2016-08-18T00:00:00Z","publication_status":"published","oa":1,"citation":{"short":"M.H. Henzinger, S. Neumann, in:, 24th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","chicago":"Henzinger, Monika H, and Stefan Neumann. “Incremental and Fully Dynamic Subgraph Connectivity for Emergency Planning.” In 24th Annual European Symposium on Algorithms, Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPICS.ESA.2016.48.","ieee":"M. H. Henzinger and S. Neumann, “Incremental and fully dynamic subgraph connectivity for emergency planning,” in 24th Annual European Symposium on Algorithms, Aarhus, Denmark, 2016, vol. 57.","apa":"Henzinger, M. H., & Neumann, S. (2016). Incremental and fully dynamic subgraph connectivity for emergency planning. In 24th Annual European Symposium on Algorithms (Vol. 57). Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2016.48","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.","mla":"Henzinger, Monika H., and Stefan Neumann. “Incremental and Fully Dynamic Subgraph Connectivity for Emergency Planning.” 24th Annual European Symposium on Algorithms, vol. 57, 48, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPICS.ESA.2016.48.","ama":"Henzinger MH, Neumann S. Incremental and fully dynamic subgraph connectivity for emergency planning. In: 24th Annual European Symposium on Algorithms. Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPICS.ESA.2016.48"},"extern":"1","intvolume":" 57","external_id":{"arxiv":["1611.05248"]},"status":"public","alternative_title":["LIPIcs"]},{"year":"2016","_id":"11836","oa_version":"Published Version","type":"conference","month":"08","date_updated":"2023-02-16T12:09:54Z","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,"external_id":{"arxiv":["1604.08342"]},"status":"public","alternative_title":["LIPIcs"],"citation":{"apa":"Cheung, Y. K., Goranci, G., & Henzinger, M. H. (2016). Graph minors for preserving terminal distances approximately - lower and upper bounds. In 43rd International Colloquium on Automata, Languages, and Programming (Vol. 55). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2016.131","mla":"Cheung, Yun Kuen, et al. “Graph Minors for Preserving Terminal Distances Approximately - Lower and Upper Bounds.” 43rd International Colloquium on Automata, Languages, and Programming, vol. 55, 131, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPICS.ICALP.2016.131.","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.","ama":"Cheung YK, Goranci G, Henzinger MH. Graph minors for preserving terminal distances approximately - lower and upper bounds. In: 43rd International Colloquium on Automata, Languages, and Programming. Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPICS.ICALP.2016.131","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.","chicago":"Cheung, Yun Kuen, Gramoz Goranci, and Monika H Henzinger. “Graph Minors for Preserving Terminal Distances Approximately - Lower and Upper Bounds.” In 43rd International Colloquium on Automata, Languages, and Programming, Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPICS.ICALP.2016.131.","ieee":"Y. K. Cheung, G. Goranci, and M. H. Henzinger, “Graph minors for preserving terminal distances approximately - lower and upper bounds,” in 43rd International Colloquium on Automata, Languages, and Programming, Rome, Italy, 2016, vol. 55."},"extern":"1","intvolume":" 55","publication_status":"published","oa":1,"main_file_link":[{"url":"https://doi.org/10.4230/LIPICS.ICALP.2016.131","open_access":"1"}],"date_published":"2016-08-23T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","scopus_import":"1","article_processing_charge":"No","publication":"43rd International Colloquium on Automata, Languages, and Programming","day":"23","author":[{"last_name":"Cheung","first_name":"Yun Kuen","full_name":"Cheung, Yun Kuen"},{"last_name":"Goranci","first_name":"Gramoz","full_name":"Goranci, Gramoz"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger"}],"article_number":"131","arxiv":1,"title":"Graph minors for preserving terminal distances approximately - lower and upper bounds","language":[{"iso":"eng"}],"conference":{"end_date":"2016-07-15","name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Rome, Italy","start_date":"2016-07-12"},"publication_identifier":{"isbn":["978-3-95977-013-2"],"issn":["1868-8969"]},"quality_controlled":"1","doi":"10.4230/LIPICS.ICALP.2016.131"},{"_id":"1184","year":"2016","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.","file_date_updated":"2020-07-14T12:44:37Z","date_created":"2018-12-11T11:50:36Z","volume":6,"month":"12","oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"date_updated":"2021-01-12T06:48:55Z","page":"8903 - 8906","citation":{"ieee":"S. Metzler, J. Heinze, and A. Schrempf, “Mating and longevity in ant males,” Ecology and Evolution, vol. 6, no. 24. Wiley-Blackwell, pp. 8903–8906, 2016.","chicago":"Metzler, Sina, Jürgen Heinze, and Alexandra Schrempf. “Mating and Longevity in Ant Males.” Ecology and Evolution. Wiley-Blackwell, 2016. https://doi.org/10.1002/ece3.2474.","short":"S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906.","ama":"Metzler S, Heinze J, Schrempf A. Mating and longevity in ant males. Ecology and Evolution. 2016;6(24):8903-8906. doi:10.1002/ece3.2474","ista":"Metzler S, Heinze J, Schrempf A. 2016. Mating and longevity in ant males. Ecology and Evolution. 6(24), 8903–8906.","mla":"Metzler, Sina, et al. “Mating and Longevity in Ant Males.” Ecology and Evolution, vol. 6, no. 24, Wiley-Blackwell, 2016, pp. 8903–06, doi:10.1002/ece3.2474.","apa":"Metzler, S., Heinze, J., & Schrempf, A. (2016). Mating and longevity in ant males. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.2474"},"intvolume":" 6","status":"public","date_published":"2016-12-01T00:00:00Z","ddc":["576","592"],"has_accepted_license":"1","oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":1,"publication":"Ecology and Evolution","department":[{"_id":"SyCr"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley-Blackwell","publist_id":"6169","title":"Mating and longevity in ant males","day":"01","file":[{"relation":"main_file","content_type":"application/pdf","file_size":328414,"creator":"system","file_name":"IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf","date_created":"2018-12-12T10:14:12Z","access_level":"open_access","date_updated":"2020-07-14T12:44:37Z","file_id":"5062","checksum":"789026eb9e1be2a0da08376f29f569cf"}],"author":[{"last_name":"Metzler","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","full_name":"Metzler, Sina"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"full_name":"Schrempf, Alexandra","first_name":"Alexandra","last_name":"Schrempf"}],"issue":"24","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1002/ece3.2474","pubrep_id":"736"},{"language":[{"iso":"eng"}],"pubrep_id":"735","doi":"10.1038/srep38094","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","department":[{"_id":"LeSa"}],"publication":"Scientific Reports","scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","full_name":"Gutierrez-Fernandez, Javier","last_name":"Gutierrez-Fernandez","first_name":"Javier"},{"first_name":"Malek","last_name":"Saleh","full_name":"Saleh, Malek"},{"first_name":"Martín","last_name":"Alcorlo","full_name":"Alcorlo, Martín"},{"full_name":"Gómez Mejóa, Alejandro","last_name":"Gómez Mejóa","first_name":"Alejandro"},{"first_name":"David","last_name":"Pantoja Uceda","full_name":"Pantoja Uceda, David"},{"full_name":"Treviño, Miguel","first_name":"Miguel","last_name":"Treviño"},{"first_name":"Franziska","last_name":"Vob","full_name":"Vob, Franziska"},{"full_name":"Abdullah, Mohammed","last_name":"Abdullah","first_name":"Mohammed"},{"full_name":"Galán Bartual, Sergio","last_name":"Galán Bartual","first_name":"Sergio"},{"first_name":"Jolien","last_name":"Seinen","full_name":"Seinen, Jolien"},{"last_name":"Sánchez Murcia","first_name":"Pedro","full_name":"Sánchez Murcia, Pedro"},{"full_name":"Gago, Federico","first_name":"Federico","last_name":"Gago"},{"full_name":"Bruix, Marta","last_name":"Bruix","first_name":"Marta"},{"full_name":"Hammerschmidt, Sven","last_name":"Hammerschmidt","first_name":"Sven"},{"first_name":"Juan","last_name":"Hermoso","full_name":"Hermoso, Juan"}],"file":[{"file_name":"IST-2017-735-v1+1_srep38094.pdf","creator":"system","file_size":2716045,"content_type":"application/pdf","relation":"main_file","checksum":"e007d78b483bc59bf5ab98e9d42a6ec1","file_id":"4804","date_updated":"2020-07-14T12:44:37Z","access_level":"open_access","date_created":"2018-12-12T10:10:18Z"}],"day":"05","title":"Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis","article_number":"38094","publist_id":"6167","status":"public","intvolume":" 6","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. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38094","mla":"Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” Scientific Reports, vol. 6, 38094, Nature Publishing Group, 2016, doi:10.1038/srep38094.","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.","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. Scientific Reports. 2016;6. doi:10.1038/srep38094","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).","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.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38094.","ieee":"J. Gutierrez-Fernandez et al., “Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016."},"publication_status":"published","oa":1,"has_accepted_license":"1","date_published":"2016-12-05T00:00:00Z","ddc":["576","610"],"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).","year":"2016","_id":"1186","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"}],"date_updated":"2021-01-12T06:48:56Z","oa_version":"Published Version","month":"12","type":"journal_article","volume":6,"file_date_updated":"2020-07-14T12:44:37Z","date_created":"2018-12-11T11:50:36Z"},{"author":[{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H"},{"first_name":"Sebastian","last_name":"Krinninger","full_name":"Krinninger, Sebastian"},{"full_name":"Nanongkai, Danupon","first_name":"Danupon","last_name":"Nanongkai"}],"day":"01","title":"A deterministic almost-tight distributed algorithm for approximating single-source shortest paths","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","publication":"48th Annual ACM SIGACT Symposium on Theory of Computing","scopus_import":"1","article_processing_charge":"No","publication_identifier":{"issn":["0737-8017"],"isbn":["978-145034132-5"]},"doi":"10.1145/2897518.2897638","quality_controlled":"1","conference":{"name":"STOC: Symposium on Theory of Computing","location":"Cambridge, MA, United States","start_date":"2016-06-19","end_date":"2016-06-21"},"language":[{"iso":"eng"}],"page":"489 - 498","type":"conference","oa_version":"Preprint","month":"06","abstract":[{"lang":"eng","text":"We present a deterministic (1+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time algorithm for solving the single-source shortest paths problem on distributed weighted networks (the CONGEST model); here n is the number of nodes in the network and D is its (hop) diameter. This is the first non-trivial deterministic algorithm for this problem. It also improves (i) the running time of the randomized (1+o(1))-approximation Õ(n1/2D1/4+D)-time algorithm of Nanongkai [STOC 2014] by a factor of as large as n1/8, and (ii) the O(є−1logє−1)-approximation factor of Lenzen and Patt-Shamir’s Õ(n1/2+є+D)-time algorithm [STOC 2013] within the same running time. Our running time matches the known time lower bound of Ω(n1/2/logn + D) [Das Sarma et al. STOC 2011] modulo some lower-order terms, thus essentially settling the status of this problem which was raised at least a decade ago [Elkin SIGACT News 2004]. It also implies a (2+o(1))-approximation O(n1/2+o(1)+D1+o(1))-time algorithm for approximating a network’s weighted diameter which almost matches the lower bound by Holzer et al. [PODC 2012].\r\n\r\nIn achieving this result, we develop two techniques which might be of independent interest and useful in other settings: (i) a deterministic process that replaces the “hitting set argument” commonly used for shortest paths computation in various settings, and (ii) a simple, deterministic, construction of an (no(1), o(1))-hop set of size O(n1+o(1)). We combine these techniques with many distributed algorithmic techniques, some of which from problems that are not directly related to shortest paths, e.g. ruling sets [Goldberg et al. STOC 1987], source detection [Lenzen, Peleg PODC 2013], and partial distance estimation [Lenzen, Patt-Shamir PODC 2015]. Our hop set construction also leads to single-source shortest paths algorithms in two other settings: (i) a (1+o(1))-approximation O(no(1))-time algorithm on congested cliques, and (ii) a (1+o(1))-approximation O(no(1)logW)-pass O(n1+o(1)logW)-space streaming algorithm, when edge weights are in {1, 2, …, W}. The first result answers an open problem in [Nanongkai, STOC 2014]. The second result partially answers an open problem raised by McGregor in 2006 [sublinear.info
, Problem 14]."}],"date_updated":"2023-02-17T10:32:23Z","date_created":"2022-08-16T09:19:31Z","year":"2016","_id":"11866","publication_status":"published","oa":1,"date_published":"2016-06-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1504.07056","open_access":"1"}],"external_id":{"arxiv":["1504.07056"]},"status":"public","extern":"1","citation":{"chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “A Deterministic Almost-Tight Distributed Algorithm for Approximating Single-Source Shortest Paths.” In 48th Annual ACM SIGACT Symposium on Theory of Computing, 489–98. Association for Computing Machinery, 2016. https://doi.org/10.1145/2897518.2897638.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “A deterministic almost-tight distributed algorithm for approximating single-source shortest paths,” in 48th Annual ACM SIGACT Symposium on Theory of Computing, 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: 48th Annual ACM SIGACT Symposium on Theory of Computing. Association for Computing Machinery; 2016:489-498. doi:10.1145/2897518.2897638","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2016). A deterministic almost-tight distributed algorithm for approximating single-source shortest paths. In 48th Annual ACM SIGACT Symposium on Theory of Computing (pp. 489–498). Cambridge, MA, United States: Association for Computing Machinery. https://doi.org/10.1145/2897518.2897638","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.","mla":"Henzinger, Monika H., et al. “A Deterministic Almost-Tight Distributed Algorithm for Approximating Single-Source Shortest Paths.” 48th Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp. 489–98, doi:10.1145/2897518.2897638."}},{"author":[{"full_name":"Bhattacharya, Sayan","first_name":"Sayan","last_name":"Bhattacharya"},{"last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"}],"day":"01","arxiv":1,"title":"New deterministic approximation algorithms for fully dynamic matching","publisher":"Association for Computing Machinery","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"48th Annual ACM SIGACT Symposium on Theory of Computing","article_processing_charge":"No","scopus_import":"1","publication_identifier":{"issn":["0737-8017"],"isbn":["978-145034132-5"]},"doi":"10.1145/2897518.2897568","quality_controlled":"1","conference":{"end_date":"2016-06-21","name":"STOC: Symposium on Theory of Computing","location":"Cambridge, MA, United States","start_date":"2016-06-19"},"language":[{"iso":"eng"}],"page":"398 - 411","month":"06","type":"conference","oa_version":"Preprint","date_updated":"2023-02-17T11:08:19Z","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."}],"date_created":"2022-08-16T09:27:35Z","year":"2016","_id":"11867","oa":1,"publication_status":"published","date_published":"2016-06-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.05765"}],"external_id":{"arxiv":["1604.05765"]},"status":"public","extern":"1","citation":{"short":"S. Bhattacharya, M.H. Henzinger, D. Nanongkai, in:, 48th Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp. 398–411.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, and Danupon Nanongkai. “New Deterministic Approximation Algorithms for Fully Dynamic Matching.” In 48th Annual ACM SIGACT Symposium on Theory of Computing, 398–411. Association for Computing Machinery, 2016. https://doi.org/10.1145/2897518.2897568.","ieee":"S. Bhattacharya, M. H. Henzinger, and D. Nanongkai, “New deterministic approximation algorithms for fully dynamic matching,” in 48th Annual ACM SIGACT Symposium on Theory of Computing, Cambridge, MA, United States, 2016, pp. 398–411.","apa":"Bhattacharya, S., Henzinger, M. H., & Nanongkai, D. (2016). New deterministic approximation algorithms for fully dynamic matching. In 48th Annual ACM SIGACT Symposium on Theory of Computing (pp. 398–411). Cambridge, MA, United States: Association for Computing Machinery. https://doi.org/10.1145/2897518.2897568","mla":"Bhattacharya, Sayan, et al. “New Deterministic Approximation Algorithms for Fully Dynamic Matching.” 48th Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2016, pp. 398–411, doi:10.1145/2897518.2897568.","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.","ama":"Bhattacharya S, Henzinger MH, Nanongkai D. New deterministic approximation algorithms for fully dynamic matching. In: 48th Annual ACM SIGACT Symposium on Theory of Computing. Association for Computing Machinery; 2016:398-411. doi:10.1145/2897518.2897568"}},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.09048"}],"date_published":"2016-12-30T00:00:00Z","oa":1,"publication_status":"published","citation":{"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 & Growth.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.","ieee":"D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016.","apa":"De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa4e8f","mla":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOPscience, 2016, doi:10.1088/1742-5468/aa4e8f.","ista":"De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.","ama":"De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f"},"intvolume":" 2016","status":"public","date_created":"2018-12-11T11:50:37Z","volume":2016,"abstract":[{"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.","lang":"eng"}],"date_updated":"2021-01-12T06:48:57Z","month":"12","type":"journal_article","oa_version":"Preprint","_id":"1188","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.","quality_controlled":"1","doi":"10.1088/1742-5468/aa4e8f","language":[{"iso":"eng"}],"issue":"12","project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"publist_id":"6165","title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth","article_number":"123502","day":"30","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele","last_name":"De Martino"},{"full_name":"Masoero, Davide","first_name":"Davide","last_name":"Masoero"}],"scopus_import":1,"ec_funded":1,"publication":" Journal of Statistical Mechanics: Theory and Experiment","department":[{"_id":"GaTk"}],"publisher":"IOPscience","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"article_processing_charge":"No","_id":"1189","year":"2016","publisher":"Technical University Vienna","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6164","date_created":"2018-12-11T11:50:37Z","title":"Dissipative Few-Body Quantum Systems","oa_version":"Published Version","type":"dissertation","month":"11","date_updated":"2021-01-12T06:48:57Z","day":"28","abstract":[{"text":"Within the scope of this thesis, we show that a driven-dissipative system with\r\nfew ultracold atoms can exhibit dissipatively bound states, even if the atom-atom\r\ninteraction is purely repulsive. This bond arises due to the dipole-dipole inter-\r\naction, which is restricted to one of the lower electronic energy states, resulting\r\nin the distance-dependent coherent population trapping. The quality of this al-\r\nready established method of dissipative binding is improved and the application\r\nis extended to higher dimensions and a larger number of atoms. Here, we simu-\r\nlate two- and three-atom systems using an adapted approach to the Monte Carlo\r\nwave-function method and analyse the results. Finally, we examine the possi-\r\nbility of finding a setting allowing trimer states but prohibiting dimer states.\r\nIn the context of open quantum systems, such a three-body bound states corre-\r\nsponds to the driven-dissipative analogue of a Borromean state. These states can\r\nbe detected in modern experiments with dipolar and Rydberg-dressed ultracold\r\natomic gases.\r\n","lang":"eng"}],"page":"94","author":[{"last_name":"Jochum","first_name":"Clemens","full_name":"Jochum, Clemens"}],"citation":{"short":"C. Jochum, Dissipative Few-Body Quantum Systems, Technical University Vienna, 2016.","chicago":"Jochum, Clemens. “Dissipative Few-Body Quantum Systems.” Technical University Vienna, 2016.","ieee":"C. Jochum, “Dissipative Few-Body Quantum Systems,” Technical University Vienna, 2016.","apa":"Jochum, C. (2016). Dissipative Few-Body Quantum Systems. Technical University Vienna.","mla":"Jochum, Clemens. Dissipative Few-Body Quantum Systems. Technical University Vienna, 2016.","ista":"Jochum C. 2016. Dissipative Few-Body Quantum Systems. Technical University Vienna.","ama":"Jochum C. Dissipative Few-Body Quantum Systems. 2016."},"language":[{"iso":"eng"}],"extern":"1","status":"public","main_file_link":[{"open_access":"1","url":"http://repositum.tuwien.ac.at/obvutwhs/content/titleinfo/1517088"}],"date_published":"2016-11-28T00:00:00Z","supervisor":[{"last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"first_name":"Peter","last_name":"Rabl","full_name":"Rabl, Peter"}],"publication_status":"published","oa":1},{"quality_controlled":"1","doi":"10.1137/140957299","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"issue":"3","language":[{"iso":"eng"}],"title":"Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization","arxiv":1,"day":"01","author":[{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"full_name":"Krinninger, Sebastian","last_name":"Krinninger","first_name":"Sebastian"},{"full_name":"Nanongkai, Danupon","first_name":"Danupon","last_name":"Nanongkai"}],"article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"SIAM Journal on Computing","publisher":"Society for Industrial & Applied Mathematics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1308.0776"}],"date_published":"2016-05-01T00:00:00Z","oa":1,"publication_status":"published","citation":{"mla":"Henzinger, Monika H., et al. “Dynamic Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.” SIAM Journal on Computing, vol. 45, no. 3, Society for Industrial & Applied Mathematics, 2016, pp. 947–1006, doi:10.1137/140957299.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2016. Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. SIAM Journal on Computing. 45(3), 947–1006.","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2016). Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/140957299","ama":"Henzinger MH, Krinninger S, Nanongkai D. Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. SIAM Journal on Computing. 2016;45(3):947-1006. doi:10.1137/140957299","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, SIAM Journal on Computing 45 (2016) 947–1006.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization,” SIAM Journal on Computing, vol. 45, no. 3. Society for Industrial & Applied Mathematics, pp. 947–1006, 2016.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Dynamic Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2016. https://doi.org/10.1137/140957299."},"extern":"1","intvolume":" 45","external_id":{"arxiv":["1308.0776"]},"status":"public","date_created":"2022-08-17T08:37:00Z","volume":45,"type":"journal_article","month":"05","oa_version":"Preprint","abstract":[{"text":"We study dynamic (1+𝜖)-approximation algorithms for the all-pairs shortest paths problem in unweighted undirected 𝑛-node 𝑚-edge graphs under edge deletions. The fastest algorithm for this problem is a randomized algorithm with a total update time of 𝑂̃ (𝑚𝑛/𝜖) and constant query time by Roditty and Zwick [SIAM J. Comput., 41 (2012), pp. 670--683]. The fastest deterministic algorithm is from a 1981 paper by Even and Shiloach [J. ACM, 28 (1981), pp. 1--4]; it has a total update time of 𝑂(𝑚𝑛2) and constant query time. We improve these results as follows: (1) We present an algorithm with a total update time of 𝑂̃ (𝑛5/2/𝜖) and constant query time that has an additive error of 2 in addition to the 1+𝜖 multiplicative error. This beats the previous 𝑂̃ (𝑚𝑛/𝜖) time when 𝑚=Ω(𝑛3/2). Note that the additive error is unavoidable since, even in the static case, an 𝑂(𝑛3−𝛿)-time (a so-called truly subcubic) combinatorial algorithm with 1+𝜖 multiplicative error cannot have an additive error less than 2−𝜖, unless we make a major breakthrough for Boolean matrix multiplication [D. Dor, S. Halrepin, and U. Zwick, SIAM J. Comput., 29 (2000), pp. 1740--1759] and many other long-standing problems [V. Vassilevska Williams and R. Williams, Proceedings of the 2010 IEEE 51st Annual Symposium on Foundations of Computer Science, 2010, pp. 645--654]. The algorithm can also be turned into a (2+𝜖)-approximation algorithm (without an additive error) with the same time guarantees, improving the recent (3+𝜖)-approximation algorithm with 𝑂̃ (𝑛5/2+𝑂(log(1/𝜖)/log𝑛√)) running time of Bernstein and Roditty [Proceedings of the Twenty-Second Annual ACM-SIAM Symposium on Discrete Algorithms, 2011, pp. 1355--1365] in terms of both approximation and time guarantees. (2) We present a deterministic algorithm with a total update time of 𝑂̃ (𝑚𝑛/𝜖) and a query time of 𝑂(loglog𝑛). The algorithm has a multiplicative error of 1+𝜖 and gives the first improved deterministic algorithm since 1981. It also answers an open question raised by Bernstein in [Proceedings of the Forty-Fifth Annual ACM Symposium on Theory of Computing, 2013, pp. 725--734]. The deterministic algorithm can be turned into a deterministic fully dynamic (1+𝜖)-approximation with an amortized update time of 𝑂̃ (𝑚𝑛/(𝜖𝑡)) and a query time of 𝑂̃ (𝑡) for every 𝑡≤𝑛√. In order to achieve our results, we introduce two new techniques: (i) A monotone Even--Shiloach tree algorithm which maintains a bounded-distance shortest-paths tree on a certain type of emulator called a locally persevering emulator. (ii) A derandomization technique based on moving Even--Shiloach trees as a way to derandomize the standard random set argument. These techniques might be of independent interest.","lang":"eng"}],"date_updated":"2023-02-17T14:21:40Z","page":"947-1006","_id":"11891","year":"2016"},{"main_file_link":[{"url":"https://arxiv.org/abs/1506.08547v7","open_access":"1"}],"date_published":"2016-12-15T00:00:00Z","publication_status":"published","oa":1,"citation":{"ieee":"V. Kolmogorov, “Commutativity in the algorithmic Lovasz local lemma,” in Proceedings - Annual IEEE Symposium on Foundations of Computer Science, New Brunswick, NJ, USA , 2016, vol. 2016–December.","chicago":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.” In Proceedings - Annual IEEE Symposium on Foundations of Computer Science, Vol. 2016–December. IEEE, 2016. https://doi.org/10.1109/FOCS.2016.88.","short":"V. Kolmogorov, in:, Proceedings - Annual IEEE Symposium on Foundations of Computer Science, IEEE, 2016.","ama":"Kolmogorov V. Commutativity in the algorithmic Lovasz local lemma. In: Proceedings - Annual IEEE Symposium on Foundations of Computer Science. Vol 2016-December. IEEE; 2016. doi:10.1109/FOCS.2016.88","mla":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.” Proceedings - Annual IEEE Symposium on Foundations of Computer Science, vol. 2016–December, 7782993, IEEE, 2016, doi:10.1109/FOCS.2016.88.","ista":"Kolmogorov V. 2016. Commutativity in the algorithmic Lovasz local lemma. Proceedings - Annual IEEE Symposium on Foundations of Computer Science. FOCS: Foundations of Computer Science vol. 2016–December, 7782993.","apa":"Kolmogorov, V. (2016). Commutativity in the algorithmic Lovasz local lemma. In Proceedings - Annual IEEE Symposium on Foundations of Computer Science (Vol. 2016–December). New Brunswick, NJ, USA : IEEE. https://doi.org/10.1109/FOCS.2016.88"},"related_material":{"record":[{"relation":"later_version","id":"5975","status":"public"}]},"status":"public","external_id":{"arxiv":["1506.08547"]},"date_created":"2018-12-11T11:50:38Z","volume":"2016-December","abstract":[{"text":"We consider the recent formulation of the Algorithmic Lovász Local Lemma [1], [2] for finding objects that avoid "bad features", or "flaws". It extends the Moser-Tardos resampling algorithm [3] to more general discrete spaces. At each step the method picks a flaw present in the current state and "resamples" it using a "resampling oracle" provided by the user. However, it is less flexible than the Moser-Tardos method since [1], [2] require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and thus can potentially be implemented more efficiently). We formulate a new "commutativity" condition, and prove that it is sufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additional assumption. We then show that existing resampling oracles for perfect matchings and permutations do satisfy this condition. Finally, we generalize the precondition in [2] (in the case of symmetric potential causality graphs). This unifies special cases that previously were treated separately.","lang":"eng"}],"date_updated":"2023-09-19T14:24:57Z","oa_version":"Preprint","type":"conference","month":"12","_id":"1193","year":"2016","acknowledgement":"European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160","quality_controlled":"1","doi":"10.1109/FOCS.2016.88","language":[{"iso":"eng"}],"conference":{"start_date":"2016-09-09","name":"FOCS: Foundations of Computer Science","location":"New Brunswick, NJ, USA ","end_date":"2016-09-11"},"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160"}],"publist_id":"6158","title":"Commutativity in the algorithmic Lovasz local lemma","arxiv":1,"article_number":"7782993","day":"15","author":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"}],"article_processing_charge":"No","ec_funded":1,"scopus_import":1,"publication":"Proceedings - Annual IEEE Symposium on Foundations of Computer Science","department":[{"_id":"VlKo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE"},{"project":[{"grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"language":[{"iso":"eng"}],"issue":"1","pubrep_id":"770","doi":"10.1093/molbev/msw210","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"publication":"Molecular Biology and Evolution","scopus_import":1,"ec_funded":1,"author":[{"full_name":"Franssen, Susan","last_name":"Franssen","first_name":"Susan"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Schlötterer, Christian","last_name":"Schlötterer","first_name":"Christian"}],"file":[{"checksum":"1e78d3aaffcb40dc8b02b7b4666019e0","file_id":"5223","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","date_created":"2018-12-12T10:16:35Z","file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","creator":"system","file_size":295274,"relation":"main_file","content_type":"application/pdf"},{"date_created":"2018-12-12T10:16:36Z","access_level":"open_access","file_id":"5224","date_updated":"2020-07-14T12:44:38Z","checksum":"e13171843283774404c936c581b4543e","file_size":10902625,"content_type":"application/pdf","relation":"main_file","creator":"system","file_name":"IST-2017-770-v1+2_Fig1.pdf"},{"file_name":"IST-2017-770-v1+3_Fig2.pdf","content_type":"application/pdf","relation":"main_file","file_size":21437,"creator":"system","date_updated":"2020-07-14T12:44:38Z","file_id":"5225","checksum":"63bc6e6e61f347594d8c00c37f874a0b","date_created":"2018-12-12T10:16:37Z","access_level":"open_access"},{"file_name":"IST-2017-770-v1+4_Fig3.pdf","creator":"system","content_type":"application/pdf","relation":"main_file","file_size":1172194,"checksum":"da87cc7c78808837f22a3dae1c8397f9","date_updated":"2020-07-14T12:44:38Z","file_id":"5226","access_level":"open_access","date_created":"2018-12-12T10:16:38Z"},{"file_name":"IST-2017-770-v1+5_Fig4.pdf","creator":"system","file_size":50045,"content_type":"application/pdf","relation":"main_file","checksum":"e47b2a0c32142f423b3100150c0294f8","file_id":"5227","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","date_created":"2018-12-12T10:16:38Z"},{"checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9","file_id":"5228","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","date_created":"2018-12-12T10:16:39Z","file_name":"IST-2017-770-v1+6_Fig5.pdf","creator":"system","file_size":50705,"content_type":"application/pdf","relation":"main_file"}],"day":"03","title":"Reconstruction of haplotype-blocks selected during experimental evolution.","publist_id":"6155","status":"public","intvolume":" 34","citation":{"ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.","mla":"Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210.","apa":"Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210","ama":"Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184. doi:10.1093/molbev/msw210","short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","ieee":"S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” Molecular Biology and Evolution, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.","chicago":"Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210."},"publication_status":"published","oa":1,"has_accepted_license":"1","ddc":["576"],"date_published":"2016-10-03T00:00:00Z","acknowledgement":"The authors thank all members of the Institute of Population\r\nGenetics for discussion and support on the project and par-\r\nticularly N. Barghi for helpful comments on earlier versions of\r\nthe manuscript. This work was supported by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”.","year":"2016","_id":"1195","page":"174 - 184","abstract":[{"lang":"eng","text":"The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. "}],"date_updated":"2021-01-12T06:49:00Z","month":"10","oa_version":"Submitted Version","type":"journal_article","volume":34,"date_created":"2018-12-11T11:50:39Z","file_date_updated":"2020-07-14T12:44:38Z"},{"acknowledgement":"JSP was supported by a C.V. Starr Fellowship from the Starr Foundation (http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation (https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler for helpful comments on the manuscript.","year":"2016","_id":"1197","month":"11","type":"journal_article","oa_version":"Published Version","abstract":[{"text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.","lang":"eng"}],"date_updated":"2023-02-23T14:05:40Z","volume":12,"date_created":"2018-12-11T11:50:40Z","file_date_updated":"2020-07-14T12:44:38Z","status":"public","related_material":{"record":[{"relation":"research_data","status":"public","id":"9709"}]},"intvolume":" 12","citation":{"chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148.","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11. Public Library of Science, 2016.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016).","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes of the retinal population code. PLoS Computational Biology. 2016;12(11). doi:10.1371/journal.pcbi.1005148","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2016). Error-robust modes of the retinal population code. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005148","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust modes of the retinal population code. 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Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze. Physics of Life Reviews. 2016;19:29-31. doi:10.1016/j.plrev.2016.10.004","apa":"Hilbe, C., & Traulsen, A. (2016). Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.10.004","mla":"Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling: Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J. Schossau and A. Hintze.” Physics of Life Reviews, vol. 19, Elsevier, 2016, pp. 29–31, doi:10.1016/j.plrev.2016.10.004.","ista":"Hilbe C, Traulsen A. 2016. Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze. Physics of Life Reviews. 19, 29–31.","chicago":"Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling: Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J. Schossau and A. Hintze.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.10.004.","ieee":"C. Hilbe and A. Traulsen, “Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on ‘Evolutionary game theory using agent-based methods’ by C. Adami, J. Schossau and A. Hintze,” Physics of Life Reviews, vol. 19. Elsevier, pp. 29–31, 2016.","short":"C. Hilbe, A. Traulsen, Physics of Life Reviews 19 (2016) 29–31."},"status":"public","volume":19,"file_date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-11T11:50:40Z","page":"29 - 31","date_updated":"2021-01-12T06:49:03Z","type":"journal_article","oa_version":"Submitted Version","month":"12","_id":"1200","acknowledgement":"C.H. acknowledges generous support from the ISTFELLOW program.","year":"2016"},{"date_published":"2016-08-01T00:00:00Z","ddc":["570"],"publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":" 119","citation":{"ista":"Milutinovic B, Peuß R, Ferro K, Kurtz J. 2016. Immune priming in arthropods: an update focusing on the red flour beetle. 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Elsevier, pp. 254–261, 2016.","chicago":"Milutinovic, Barbara, Robert Peuß, Kevin Ferro, and Joachim Kurtz. “Immune Priming in Arthropods: An Update Focusing on the Red Flour Beetle.” Zoology . Elsevier, 2016. https://doi.org/10.1016/j.zool.2016.03.006."},"status":"public","volume":119,"file_date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-11T11:50:41Z","page":"254 - 261","oa_version":"Published Version","month":"08","type":"journal_article","date_updated":"2021-01-12T06:49:03Z","_id":"1202","acknowledgement":"The authors thank Sophie A.O. Armitage and Jan N. Offenborn for helpful comments on the figures, and two anonymous reviewers for their helpful comments. The project was funded by the Deutsche Forschungsgemeinschaft (DFG, KU 1929/4-2) within the priority programme SPP 1399 “Host–Parasite Coevolution”.","year":"2016","doi":"10.1016/j.zool.2016.03.006","quality_controlled":"1","issue":"4","language":[{"iso":"eng"}],"project":[{"grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"}],"title":"Immune priming in arthropods: an update focusing on the red flour beetle","publist_id":"6147","author":[{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara","last_name":"Milutinovic","first_name":"Barbara"},{"full_name":"Peuß, Robert","first_name":"Robert","last_name":"Peuß"},{"full_name":"Ferro, Kevin","last_name":"Ferro","first_name":"Kevin"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"}],"day":"01","file":[{"file_name":"2016_Elsevier_Milutinovic.pdf","file_size":1473211,"relation":"main_file","content_type":"application/pdf","creator":"kschuh","file_id":"5885","date_updated":"2020-07-14T12:44:39Z","checksum":"8396d5bd95f9c4295857162f902afabf","date_created":"2019-01-25T13:00:20Z","access_level":"open_access"}],"publication":"Zoology ","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"scopus_import":1,"publisher":"Elsevier","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SyCr"}]},{"date_published":"2016-12-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121393/"}],"oa":1,"publication_status":"published","intvolume":" 54","citation":{"chicago":"Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology. American Society for Microbiology, 2016. https://doi.org/10.1128/JCM.01511-16.","ieee":"F. Hu et al., “Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,” Journal of Clinical Microbiology, vol. 54, no. 12. American Society for Microbiology, pp. 3010–3017, 2016.","short":"F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.","ama":"Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 2016;54(12):3010-3017. doi:10.1128/JCM.01511-16","apa":"Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., … Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. American Society for Microbiology. https://doi.org/10.1128/JCM.01511-16","ista":"Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 54(12), 3010–3017.","mla":"Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology, vol. 54, no. 12, American Society for Microbiology, 2016, pp. 3010–17, doi:10.1128/JCM.01511-16."},"status":"public","volume":54,"date_created":"2018-12-11T11:50:41Z","page":"3010 - 3017","oa_version":"Submitted Version","month":"12","type":"journal_article","date_updated":"2021-01-12T06:49:04Z","abstract":[{"lang":"eng","text":"Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus. Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus. A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae."}],"_id":"1203","acknowledgement":"We are grateful to ABCs for providing strains and the Bacterial Meningitis Laboratory for technical support.","year":"2016","doi":"10.1128/JCM.01511-16","quality_controlled":"1","issue":"12","language":[{"iso":"eng"}],"title":"Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination","publist_id":"6146","author":[{"full_name":"Hu, Fang","last_name":"Hu","first_name":"Fang"},{"first_name":"Lavanya","last_name":"Rishishwar","full_name":"Rishishwar, Lavanya"},{"full_name":"Sivadas, Ambily","first_name":"Ambily","last_name":"Sivadas"},{"first_name":"Gabriel","last_name":"Mitchell","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","full_name":"Mitchell, Gabriel"},{"full_name":"King, Jordan","last_name":"King","first_name":"Jordan"},{"full_name":"Murphy, Timothy","last_name":"Murphy","first_name":"Timothy"},{"full_name":"Gilsdorf, Janet","first_name":"Janet","last_name":"Gilsdorf"},{"full_name":"Mayer, Leonard","first_name":"Leonard","last_name":"Mayer"},{"first_name":"Xin","last_name":"Wang","full_name":"Wang, Xin"}],"day":"01","publication":"Journal of Clinical Microbiology","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Society for Microbiology","department":[{"_id":"GaTk"}]}]