[{"scopus_import":"1","date_created":"2018-12-11T11:46:50Z","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"       268","abstract":[{"text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry.","lang":"eng"}],"publication":"Journal of Biotechnology","publist_id":"7317","status":"public","date_published":"2018-02-20T00:00:00Z","publication_status":"published","publisher":"Elsevier","acknowledged_ssus":[{"_id":"Bio"}],"department":[{"_id":"CaGu"}],"quality_controlled":"1","type":"journal_article","volume":268,"citation":{"ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. 2018;268:40-52. doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>","ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.","apa":"Tomasek, K., Bergmiller, T., &#38; Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>","chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>.","ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” <i>Journal of Biotechnology</i>, vol. 268. Elsevier, pp. 40–52, 2018.","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>, vol. 268, Elsevier, 2018, pp. 40–52, doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>."},"author":[{"orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet"}],"month":"02","language":[{"iso":"eng"}],"_id":"503","acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n","page":"40 - 52","day":"20","date_updated":"2023-09-13T08:24:51Z","doi":"10.1016/j.jbiotec.2018.01.008","title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","external_id":{"isi":["000425715100006"]},"isi":1,"article_processing_charge":"No","year":"2018"},{"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"RySh"}],"supervisor":[{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:44:22Z","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Asymmetries have long been known about in the central nervous system. From gross anatomical differences, such as the presence of the parapineal organ in only one hemisphere of the developing zebrafish, to more subtle differences in activity between both hemispheres, as seen in freely roaming animals or human participants under PET and fMRI imaging analysis. The presence of asymmetries has been demonstrated to have huge behavioural implications, with their disruption often leading to the generation of neurological disorders, memory problems, changes in personality, and in an organism's health and well-being. For my Ph.D. work I aimed to tackle two important avenues of research. The first being the process of input-side dependency in the hippocampus, with the goal of finding a key gene responsible for its development (Gene X). The second project was to do with experience-induced laterality formation in the hippocampus. Specifically, how laterality in the synapse density of the CA1 stratum radiatum (s.r.) could be induced purely through environmental enrichment. Through unilateral tracer injections into the CA3, I was able to selectively measure the properties of synapses within the CA1 and investigate how they differed based upon which hemisphere the presynaptic neurone originated. Having found the existence of a previously unreported reversed (left-isomerism) i.v. mutant, through morpholocal examination of labelled terminals in the CA1 s.r., I aimed to elucidate a key gene responsible for the process of left or right determination of inputs to the CA1 s.r.. This work relates to the previous finding of input-side dependent asymmetry in the wild-type rodent, where the origin of the projecting neurone to the CA1 will determine the morphology of a synapse, to a greater degree than the hemisphere in which the projection terminates. Using left- and right-isomerism i.v. mice, in combination with whole genome sequence analysis, I highlight Ena/VASP-like (Evl) as a potential target for Gene X. In relation to this topic, I also highlight my work in the recently published paper of how knockout of PirB can lead to a lack of input-side dependency in the murine hippocampus. For the second question, I show that the environmental enrichment paradigm will lead to an asymmetry in the synapse densities in the hippocampus of mice. I also highlight that the nature of the enrichment is of less consequence than the process of enrichment itself. I demonstrate that the CA3 region will dramatically alter its projection targets, in relation to environmental stimulation, with the asymmetry in synaptic density, caused by enrichment, relying heavily on commissural fibres. I also highlight the vital importance of input-side dependent asymmetry, as a necessary component of experience-dependent laterality formation in the CA1 s.r.. However, my results suggest that it isn't the only cause, as there appears to be a CA1 dependent mechanism also at play. Upon further investigation, I highlight the significant, and highly important, finding that the changes seen in the CA1 s.r. were predominantly caused through projections from the left-CA3, with the right-CA3 having less involvement in this mechanism."}],"status":"public","date_published":"2018-06-27T00:00:00Z","publist_id":"8003","publication_identifier":{"issn":["2663-337X"]},"day":"27","date_updated":"2023-09-07T12:39:22Z","title":"From the left to the right: A tale of asymmetries, environments, and hippocampal development","doi":"10.15479/AT:ISTA:th_1032","article_processing_charge":"No","oa":1,"related_material":{"record":[{"status":"public","id":"682","relation":"part_of_dissertation"}]},"has_accepted_license":"1","year":"2018","citation":{"ama":"Case MJ. From the left to the right: A tale of asymmetries, environments, and hippocampal development. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1032\">10.15479/AT:ISTA:th_1032</a>","ista":"Case MJ. 2018. From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria.","apa":"Case, M. J. (2018). <i>From the left to the right: A tale of asymmetries, environments, and hippocampal development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1032\">https://doi.org/10.15479/AT:ISTA:th_1032</a>","chicago":"Case, Matthew J. “From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1032\">https://doi.org/10.15479/AT:ISTA:th_1032</a>.","ieee":"M. J. Case, “From the left to the right: A tale of asymmetries, environments, and hippocampal development,” Institute of Science and Technology Austria, 2018.","mla":"Case, Matthew J. <i>From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1032\">10.15479/AT:ISTA:th_1032</a>.","short":"M.J. Case, From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development, Institute of Science and Technology Austria, 2018."},"ddc":["571","576"],"month":"06","file_date_updated":"2021-02-11T23:30:13Z","author":[{"full_name":"Case, Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","last_name":"Case"}],"file":[{"checksum":"dcc7b55619d8509dd62b8e99d6cdee44","creator":"dernst","relation":"source_file","file_name":"2018_Thesis_Case_Source.doc","content_type":"application/msword","date_updated":"2021-02-11T23:30:13Z","embargo_to":"open_access","date_created":"2019-04-09T07:16:26Z","access_level":"closed","file_id":"6251","file_size":141270528},{"access_level":"open_access","date_updated":"2021-02-11T11:17:14Z","date_created":"2019-04-09T07:16:23Z","file_size":15193621,"file_id":"6252","embargo":"2019-07-05","relation":"main_file","file_name":"2018_Thesis_Case.pdf","checksum":"f69fdd5c8709c4e618aa8c1a1221153d","creator":"dernst","content_type":"application/pdf"}],"degree_awarded":"PhD","pubrep_id":"1032","_id":"51","language":[{"iso":"eng"}],"page":"186"},{"citation":{"apa":"Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. <i>Journal of Magnetism and Magnetic Materials</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">https://doi.org/10.1016/j.jmmm.2017.12.073</a>","ista":"Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441.","ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. <i>Journal of Magnetism and Magnetic Materials</i>. 2018;452:427-441. doi:<a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">10.1016/j.jmmm.2017.12.073</a>","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","mla":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” <i>Journal of Magnetism and Magnetic Materials</i>, vol. 452, Elsevier, 2018, pp. 427–41, doi:<a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">10.1016/j.jmmm.2017.12.073</a>.","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” <i>Journal of Magnetism and Magnetic Materials</i>, vol. 452. Elsevier, pp. 427–441, 2018.","chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” <i>Journal of Magnetism and Magnetic Materials</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">https://doi.org/10.1016/j.jmmm.2017.12.073</a>."},"ddc":["530"],"article_type":"original","month":"04","file_date_updated":"2020-07-14T12:46:37Z","file":[{"relation":"main_file","file_name":"2018_Magnetism_Altmeyer.pdf","checksum":"431f5cd4a628d7ca21161f82b14ccb4f","creator":"dernst","content_type":"application/pdf","access_level":"open_access","date_created":"2020-05-14T14:41:17Z","date_updated":"2020-07-14T12:46:37Z","file_size":17309535,"file_id":"7838"}],"author":[{"full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","first_name":"Sebastian","last_name":"Altmeyer","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","_id":"519","language":[{"iso":"eng"}],"page":"427 - 441","date_updated":"2023-09-13T09:03:44Z","day":"15","isi":1,"external_id":{"isi":["000425547700061"]},"title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","doi":"10.1016/j.jmmm.2017.12.073","article_processing_charge":"No","oa":1,"year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:46:56Z","scopus_import":"1","oa_version":"Submitted Version","intvolume":"       452","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-04-15T00:00:00Z","status":"public","publication":"Journal of Magnetism and Magnetic Materials","publist_id":"7297","abstract":[{"lang":"eng","text":"This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. "}],"publisher":"Elsevier","publication_status":"published","quality_controlled":"1","department":[{"_id":"BjHo"}],"volume":452,"type":"journal_article"},{"oa":1,"article_processing_charge":"No","year":"2018","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"5856","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"154"},{"id":"1198","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"741","relation":"part_of_dissertation"}]},"date_updated":"2023-09-27T12:34:14Z","day":"04","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th_1043","title":"Point interactions in systems of fermions","_id":"52","pubrep_id":"1043","language":[{"iso":"eng"}],"degree_awarded":"PhD","page":"115","ddc":["515","530","519"],"citation":{"ieee":"T. Moser, “Point interactions in systems of fermions,” Institute of Science and Technology Austria, 2018.","chicago":"Moser, Thomas. “Point Interactions in Systems of Fermions.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1043\">https://doi.org/10.15479/AT:ISTA:th_1043</a>.","short":"T. Moser, Point Interactions in Systems of Fermions, Institute of Science and Technology Austria, 2018.","mla":"Moser, Thomas. <i>Point Interactions in Systems of Fermions</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1043\">10.15479/AT:ISTA:th_1043</a>.","ama":"Moser T. Point interactions in systems of fermions. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1043\">10.15479/AT:ISTA:th_1043</a>","apa":"Moser, T. (2018). <i>Point interactions in systems of fermions</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1043\">https://doi.org/10.15479/AT:ISTA:th_1043</a>","ista":"Moser T. 2018. Point interactions in systems of fermions. Institute of Science and Technology Austria."},"author":[{"first_name":"Thomas","last_name":"Moser","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","full_name":"Moser, Thomas"}],"file":[{"file_size":851164,"file_id":"6256","access_level":"open_access","date_updated":"2020-07-14T12:46:37Z","date_created":"2019-04-09T07:45:38Z","content_type":"application/pdf","relation":"main_file","file_name":"2018_Thesis_Moser.pdf","checksum":"fbd8c747d148b468a21213b7cf175225","creator":"dernst"},{"content_type":"application/zip","checksum":"c28e16ecfc1126d3ce324ec96493c01e","creator":"dernst","file_name":"2018_Thesis_Moser_Source.zip","relation":"source_file","file_id":"6257","file_size":1531516,"date_updated":"2020-07-14T12:46:37Z","date_created":"2019-04-09T07:45:38Z","access_level":"closed"}],"month":"09","file_date_updated":"2020-07-14T12:46:37Z","type":"dissertation","publisher":"Institute of Science and Technology Austria","publication_status":"published","project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27"}],"supervisor":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer"}],"department":[{"_id":"RoSe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8002","date_published":"2018-09-04T00:00:00Z","status":"public","abstract":[{"text":"In this thesis we will discuss systems of point interacting fermions, their stability and other spectral properties. Whereas for bosons a point interacting system is always unstable this ques- tion is more subtle for a gas of two species of fermions. In particular the answer depends on the mass ratio between these two species. Most of this work will be focused on the N + M model which consists of two species of fermions with N, M particles respectively which interact via point interactions. We will introduce this model using a formal limit and discuss the N + 1 system in more detail. In particular, we will show that for mass ratios above a critical one, which does not depend on the particle number, the N + 1 system is stable. In the context of this model we will prove rigorous versions of Tan relations which relate various quantities of the point-interacting model. By restricting the N + 1 system to a box we define a finite density model with point in- teractions. In the context of this system we will discuss the energy change when introducing a point-interacting impurity into a system of non-interacting fermions. We will see that this change in energy is bounded independently of the particle number and in particular the bound only depends on the density and the scattering length. As another special case of the N + M model we will show stability of the 2 + 2 model for mass ratios in an interval around one. Further we will investigate a different model of point interactions which was discussed before in the literature and which is, contrary to the N + M model, not given by a limiting procedure but is based on a Dirichlet form. We will show that this system behaves trivially in the thermodynamic limit, i.e. the free energy per particle is the same as the one of the non-interacting system.","lang":"eng"}],"date_created":"2018-12-11T11:44:22Z","alternative_title":["ISTA Thesis"],"oa_version":"Published Version"},{"volume":68,"type":"journal_article","publisher":"Elsevier","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","department":[{"_id":"HeEd"}],"intvolume":"        68","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-03-01T00:00:00Z","status":"public","publication":"Computational Geometry: Theory and Applications","publist_id":"7289","abstract":[{"text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software.","lang":"eng"}],"date_created":"2018-12-11T11:46:59Z","scopus_import":"1","oa_version":"Preprint","oa":1,"article_processing_charge":"No","ec_funded":1,"year":"2018","has_accepted_license":"1","date_updated":"2023-09-13T08:59:00Z","day":"01","isi":1,"external_id":{"isi":["000415778300010"]},"title":"Multiple covers with balls I: Inclusion–exclusion","doi":"10.1016/j.comgeo.2017.06.014","language":[{"iso":"eng"}],"_id":"530","page":"119 - 133","citation":{"chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">https://doi.org/10.1016/j.comgeo.2017.06.014</a>.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” <i>Computational Geometry: Theory and Applications</i>, vol. 68. Elsevier, pp. 119–133, 2018.","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” <i>Computational Geometry: Theory and Applications</i>, vol. 68, Elsevier, 2018, pp. 119–33, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">10.1016/j.comgeo.2017.06.014</a>.","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. <i>Computational Geometry: Theory and Applications</i>. 2018;68:119-133. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">10.1016/j.comgeo.2017.06.014</a>","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.","apa":"Edelsbrunner, H., &#38; Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">https://doi.org/10.1016/j.comgeo.2017.06.014</a>"},"ddc":["000"],"file_date_updated":"2020-07-14T12:46:38Z","month":"03","file":[{"file_name":"2018_Edelsbrunner.pdf","relation":"main_file","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","creator":"dernst","content_type":"application/pdf","access_level":"open_access","date_created":"2019-02-12T06:47:52Z","date_updated":"2020-07-14T12:46:38Z","file_size":708357,"file_id":"5953"}],"author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Iglesias Ham","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel"}]},{"type":"journal_article","volume":31,"department":[{"_id":"DaAl"}],"quality_controlled":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication_status":"published","publisher":"Springer","abstract":[{"lang":"eng","text":"We consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary. We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(nlog3n) messages in expectation, which is again within logarithmic factors of optimal. We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model."}],"publist_id":"7281","publication":"Distributed Computing","date_published":"2018-11-01T00:00:00Z","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        31","oa_version":"Published Version","scopus_import":1,"date_created":"2018-12-11T11:47:01Z","has_accepted_license":"1","year":"2018","article_processing_charge":"Yes (via OA deal)","oa":1,"doi":"10.1007/s00446-017-0315-1","title":"Communication-efficient randomized consensus","day":"01","publication_identifier":{"issn":["01782770"]},"date_updated":"2023-02-23T12:23:25Z","page":"489-501","issue":"6","_id":"536","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_name":"2017_DistribComp_Alistarh.pdf","creator":"dernst","checksum":"69b46e537acdcac745237ddb853fcbb5","file_size":595707,"file_id":"5867","access_level":"open_access","date_created":"2019-01-22T07:25:51Z","date_updated":"2020-07-14T12:46:38Z"}],"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"James","last_name":"Aspnes","full_name":"Aspnes, James"},{"first_name":"Valerie","last_name":"King","full_name":"King, Valerie"},{"full_name":"Saia, Jared","last_name":"Saia","first_name":"Jared"}],"file_date_updated":"2020-07-14T12:46:38Z","month":"11","ddc":["000"],"citation":{"apa":"Alistarh, D.-A., Aspnes, J., King, V., &#38; Saia, J. (2018). Communication-efficient randomized consensus. <i>Distributed Computing</i>. Springer. <a href=\"https://doi.org/10.1007/s00446-017-0315-1\">https://doi.org/10.1007/s00446-017-0315-1</a>","ista":"Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized consensus. Distributed Computing. 31(6), 489–501.","ama":"Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. <i>Distributed Computing</i>. 2018;31(6):489-501. doi:<a href=\"https://doi.org/10.1007/s00446-017-0315-1\">10.1007/s00446-017-0315-1</a>","mla":"Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.” <i>Distributed Computing</i>, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:<a href=\"https://doi.org/10.1007/s00446-017-0315-1\">10.1007/s00446-017-0315-1</a>.","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 489–501.","ieee":"D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” <i>Distributed Computing</i>, vol. 31, no. 6. Springer, pp. 489–501, 2018.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” <i>Distributed Computing</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00446-017-0315-1\">https://doi.org/10.1007/s00446-017-0315-1</a>."}},{"intvolume":"        50","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2017-12-18T00:00:00Z","publication":"Nature Genetics","abstract":[{"text":"DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants.","lang":"eng"}],"date_created":"2023-01-16T09:18:05Z","scopus_import":"1","oa_version":"None","volume":50,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/"}],"publisher":"Nature Research","publication_status":"published","pmid":1,"quality_controlled":"1","department":[{"_id":"XiFe"}],"acknowledgement":"We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W.","language":[{"iso":"eng"}],"_id":"12193","issue":"1","page":"130-137","citation":{"short":"J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137.","mla":"Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>.","chicago":"Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>. Nature Research, 2017. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>.","ieee":"J. Walker <i>et al.</i>, “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” <i>Nature Genetics</i>, vol. 50, no. 1. Nature Research, pp. 130–137, 2017.","ista":"Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137.","apa":"Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., &#38; Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>","ama":"Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. 2017;50(1):130-137. doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>"},"keyword":["Genetics"],"article_type":"original","month":"12","author":[{"full_name":"Walker, James","last_name":"Walker","first_name":"James"},{"full_name":"Gao, Hongbo","first_name":"Hongbo","last_name":"Gao"},{"first_name":"Jingyi","last_name":"Zhang","full_name":"Zhang, Jingyi"},{"full_name":"Aldridge, Billy","first_name":"Billy","last_name":"Aldridge"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"full_name":"Higgins, James D.","first_name":"James D.","last_name":"Higgins"},{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"}],"oa":1,"article_processing_charge":"No","year":"2017","date_updated":"2023-10-18T07:21:53Z","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"day":"18","external_id":{"pmid":["29255257"]},"title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","doi":"10.1038/s41588-017-0008-5"},{"date_published":"2017-01-01T00:00:00Z","status":"public","publication":"European Journal of Neuroscience","publist_id":"6106","abstract":[{"lang":"eng","text":"Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        45","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","date_created":"2018-12-11T11:50:50Z","scopus_import":"1","volume":45,"type":"journal_article","pmid":1,"quality_controlled":"1","department":[{"_id":"GaNo"}],"publisher":"Wiley-Blackwell","publication_status":"published","issue":"1","page":"45 - 57","acknowledgement":"This work was supported by grants of the Austrian Science Fund (FWF) P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs- und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W.","_id":"1228","language":[{"iso":"eng"}],"pubrep_id":"738","month":"01","file_date_updated":"2020-07-14T12:44:39Z","author":[{"full_name":"Sauerzopf, Ulrich","first_name":"Ulrich","last_name":"Sauerzopf"},{"full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto","last_name":"Sacco"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"},{"full_name":"Niello, Marco","first_name":"Marco","last_name":"Niello"},{"last_name":"Weidenauer","first_name":"Ana","full_name":"Weidenauer, Ana"},{"full_name":"Praschak Rieder, Nicole","first_name":"Nicole","last_name":"Praschak Rieder"},{"full_name":"Sitte, Harald","last_name":"Sitte","first_name":"Harald"},{"last_name":"Willeit","first_name":"Matthaeus","full_name":"Willeit, Matthaeus"}],"file":[{"content_type":"application/pdf","checksum":"c572cf02be8fbb7020cfcfb892182e4c","creator":"system","file_name":"IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf","relation":"main_file","file_id":"4838","file_size":169145,"date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:10:48Z","access_level":"open_access"}],"citation":{"ama":"Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. 2017;45(1):45-57. doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>","apa":"Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>","ista":"Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 45(1), 45–57.","ieee":"U. Sauerzopf <i>et al.</i>, “Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence,” <i>European Journal of Neuroscience</i>, vol. 45, no. 1. Wiley-Blackwell, pp. 45–57, 2017.","chicago":"Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer, Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>.","short":"U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57.","mla":"Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>, vol. 45, no. 1, Wiley-Blackwell, 2017, pp. 45–57, doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>."},"ddc":["616"],"article_type":"review","year":"2017","has_accepted_license":"1","oa":1,"article_processing_charge":"No","isi":1,"external_id":{"pmid":["27690184"],"isi":["000392487100005"]},"title":"Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence","doi":"10.1111/ejn.13418","date_updated":"2023-09-20T11:16:01Z","day":"01"},{"date_updated":"2023-09-20T11:15:31Z","day":"01","isi":1,"external_id":{"isi":["000388430000011"]},"title":"Trading performance for stability in Markov decision processes","doi":"10.1016/j.jcss.2016.09.009","oa":1,"article_processing_charge":"No","year":"2017","ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","id":"2305","status":"public"}]},"has_accepted_license":"1","citation":{"ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. 2017;84:144-170. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 84, 144–170.","apa":"Brázdil, T., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2017). Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>.","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” <i>Journal of Computer and System Sciences</i>, vol. 84. Elsevier, pp. 144–170, 2017.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170.","mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>, vol. 84, Elsevier, 2017, pp. 144–70, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>."},"ddc":["004","006"],"file_date_updated":"2020-07-14T12:44:42Z","month":"03","author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Forejt","first_name":"Vojtěch","full_name":"Forejt, Vojtěch"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"}],"file":[{"relation":"main_file","file_name":"IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf","checksum":"91271b23cf884d7c06d33bef0cd623b1","creator":"system","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:11:30Z","date_updated":"2020-07-14T12:44:42Z","file_size":708657,"file_id":"4885"}],"_id":"1294","pubrep_id":"717","language":[{"iso":"eng"}],"page":"144 - 170","publisher":"Elsevier","publication_status":"published","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","department":[{"_id":"KrCh"}],"volume":84,"type":"journal_article","date_created":"2018-12-11T11:51:12Z","scopus_import":"1","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        84","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2017-03-01T00:00:00Z","status":"public","publication":"Journal of Computer and System Sciences","publist_id":"6009","abstract":[{"text":"We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints.","lang":"eng"}]},{"external_id":{"arxiv":["1701.05738"]},"doi":"10.1007/978-3-662-54577-5_26","title":"Index appearance record for transforming Rabin automata into parity automata","date_updated":"2023-06-21T13:29:46Z","day":"31","publication_identifier":{"issn":["0302-9743"],"isbn":["9783662545768"],"eisbn":["9783662545775"],"eissn":["1611-3349"]},"year":"2017","conference":{"start_date":"2017-04-22","end_date":"2017-04-29","location":"Uppsala, Sweden","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"oa":1,"article_processing_charge":"No","author":[{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias","last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias"},{"full_name":"Waldmann, Clara","last_name":"Waldmann","first_name":"Clara"},{"full_name":"Weininger, Maximilian","first_name":"Maximilian","last_name":"Weininger"}],"month":"03","arxiv":1,"citation":{"apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., &#38; Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>","ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.","ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 10205. Springer; 2017:443-460. doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>","mla":"Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 10205, Springer, 2017, pp. 443–60, doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>.","short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460.","ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, 10205:443–60. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>."},"page":"443-460","_id":"13160","language":[{"iso":"eng"}],"acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","quality_controlled":"1","department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1701.05738","open_access":"1"}],"type":"conference","volume":10205,"oa_version":"Preprint","date_created":"2023-06-21T13:21:14Z","alternative_title":["LNCS"],"publication":"Tools and Algorithms for the Construction and Analysis of Systems","status":"public","date_published":"2017-03-31T00:00:00Z","abstract":[{"lang":"eng","text":"Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae."}],"intvolume":"     10205","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"has_accepted_license":"1","year":"2017","ec_funded":1,"article_processing_charge":"No","oa":1,"title":"The lac operon in the wild","doi":"10.15479/AT:ISTA:th_857","publication_identifier":{"issn":["2663-337X"]},"day":"25","date_updated":"2023-09-07T12:01:21Z","page":"87","degree_awarded":"PhD","acknowledgement":"ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. ","_id":"820","pubrep_id":"857","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:10Z","month":"08","file":[{"date_created":"2018-12-12T10:17:00Z","date_updated":"2020-07-14T12:48:10Z","access_level":"open_access","file_id":"5252","file_size":3417773,"creator":"system","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","relation":"main_file","file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","content_type":"application/pdf"},{"content_type":"application/x-tex","file_name":"2017_thesis_Jesse_source.tex","relation":"source_file","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","creator":"dernst","file_size":215899,"file_id":"6212","access_level":"closed","date_updated":"2020-07-14T12:48:10Z","date_created":"2019-04-05T08:51:59Z"}],"author":[{"last_name":"Jesse","first_name":"Fabienne","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","full_name":"Jesse, Fabienne"}],"citation":{"ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","apa":"Jesse, F. (2017). <i>The lac operon in the wild</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">https://doi.org/10.15479/AT:ISTA:th_857</a>","ama":"Jesse F. The lac operon in the wild. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">10.15479/AT:ISTA:th_857</a>","mla":"Jesse, Fabienne. <i>The Lac Operon in the Wild</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">10.15479/AT:ISTA:th_857</a>.","short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017.","chicago":"Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">https://doi.org/10.15479/AT:ISTA:th_857</a>.","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017."},"ddc":["576","577","579"],"type":"dissertation","department":[{"_id":"JoBo"}],"supervisor":[{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background.","lang":"eng"}],"status":"public","date_published":"2017-08-25T00:00:00Z","publist_id":"6829","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:48:41Z"},{"oa_version":"Published Version","date_created":"2018-12-11T11:48:41Z","alternative_title":["ISTA Thesis"],"status":"public","date_published":"2017-08-09T00:00:00Z","publist_id":"6828","abstract":[{"lang":"eng","text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between  traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method  called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games."}],"tmp":{"image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"license":"https://creativecommons.org/licenses/by-nd/4.0/","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"department":[{"_id":"KrCh"}],"supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","type":"dissertation","file_date_updated":"2020-07-14T12:48:10Z","month":"08","file":[{"file_id":"4900","file_size":4103115,"date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-12T10:11:44Z","access_level":"open_access","content_type":"application/pdf","checksum":"3a3ec003f6ee73f41f82a544d63dfc77","creator":"system","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","relation":"main_file"},{"relation":"source_file","file_name":"2017_thesis_Pavlogiannis.zip","creator":"dernst","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","content_type":"application/zip","access_level":"closed","date_updated":"2020-07-14T12:48:10Z","date_created":"2019-04-05T07:59:31Z","file_size":14744374,"file_id":"6201"}],"author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"citation":{"ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","chicago":"Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">https://doi.org/10.15479/AT:ISTA:th_854</a>.","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017.","mla":"Pavlogiannis, Andreas. <i>Algorithmic Advances in Program Analysis and Their Applications</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>.","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>","apa":"Pavlogiannis, A. (2017). <i>Algorithmic advances in program analysis and their applications</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">https://doi.org/10.15479/AT:ISTA:th_854</a>","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria."},"ddc":["000"],"page":"418","acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here.  I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta,  Arjun Radhakrishna,  Petr Novontý,  Christian Hilbe,  Jakob Ruess,  Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey.  Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","pubrep_id":"854","_id":"821","language":[{"iso":"eng"}],"degree_awarded":"PhD","title":"Algorithmic advances in program analysis and their applications","doi":"10.15479/AT:ISTA:th_854","date_updated":"2023-09-07T12:01:59Z","publication_identifier":{"issn":["2663-337X"]},"day":"09","ec_funded":1,"year":"2017","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"1071","relation":"part_of_dissertation"},{"status":"public","id":"1437","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1602"},{"relation":"part_of_dissertation","id":"1604","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1607"},{"relation":"part_of_dissertation","id":"1714","status":"public"}]},"oa":1,"article_processing_charge":"No"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"       114","abstract":[{"text":"Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. ","lang":"eng"}],"status":"public","date_published":"2017-10-03T00:00:00Z","publist_id":"6827","publication":"PNAS","scopus_import":"1","date_created":"2018-12-11T11:48:41Z","oa_version":"Submitted Version","volume":114,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/"}],"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"ToBo"}],"pmid":1,"project":[{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","name":"Optimality principles in responses to antibiotics","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"}],"quality_controlled":"1","language":[{"iso":"eng"}],"_id":"822","page":"10666 - 10671","issue":"40","citation":{"ama":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. <i>PNAS</i>. 2017;114(40):10666-10671. doi:<a href=\"https://doi.org/10.1073/pnas.1713372114\">10.1073/pnas.1713372114</a>","apa":"de Vos, M., Zagórski, M. P., Mcnally, A., &#38; Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713372114\">https://doi.org/10.1073/pnas.1713372114</a>","ista":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671.","ieee":"M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” <i>PNAS</i>, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017.","chicago":"Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1713372114\">https://doi.org/10.1073/pnas.1713372114</a>.","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.","mla":"de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” <i>PNAS</i>, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:<a href=\"https://doi.org/10.1073/pnas.1713372114\">10.1073/pnas.1713372114</a>."},"month":"10","author":[{"full_name":"De Vos, Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","first_name":"Marjon","last_name":"De Vos"},{"full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alan","last_name":"Mcnally","full_name":"Mcnally, Alan"},{"first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X"}],"article_processing_charge":"No","oa":1,"ec_funded":1,"year":"2017","publication_identifier":{"issn":["00278424"]},"day":"03","date_updated":"2023-09-26T16:18:48Z","title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","doi":"10.1073/pnas.1713372114","isi":1,"external_id":{"pmid":["28923953"],"isi":["000412130500061"]}},{"date_updated":"2023-09-26T16:18:12Z","publication_identifier":{"issn":["17425468"]},"day":"26","isi":1,"external_id":{"isi":["000411842900001"]},"title":"Phase transitions in integer linear problems","doi":"10.1088/1742-5468/aa85c3","oa":1,"article_processing_charge":"No","ec_funded":1,"year":"2017","citation":{"short":"S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari,  Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).","mla":"Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2017, no. 9, 093404, IOPscience, 2017, doi:<a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">10.1088/1742-5468/aa85c3</a>.","ieee":"S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2017, no. 9. IOPscience, 2017.","chicago":"Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience, 2017. <a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">https://doi.org/10.1088/1742-5468/aa85c3</a>.","apa":"Colabrese, S., De Martino, D., Leuzzi, L., &#38; Marinari, E. (2017). Phase transitions in integer linear problems. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience. <a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">https://doi.org/10.1088/1742-5468/aa85c3</a>","ista":"Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems.  Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404.","ama":"Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. 2017;2017(9). doi:<a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">10.1088/1742-5468/aa85c3</a>"},"article_number":"093404","month":"09","author":[{"first_name":"Simona","last_name":"Colabrese","full_name":"Colabrese, Simona"},{"first_name":"Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele"},{"full_name":"Leuzzi, Luca","last_name":"Leuzzi","first_name":"Luca"},{"full_name":"Marinari, Enzo","first_name":"Enzo","last_name":"Marinari"}],"_id":"823","language":[{"iso":"eng"}],"issue":"9","publisher":"IOPscience","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","department":[{"_id":"GaTk"}],"volume":2017,"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1705.06303","open_access":"1"}],"date_created":"2018-12-11T11:48:41Z","scopus_import":"1","oa_version":"Submitted Version","intvolume":"      2017","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","date_published":"2017-09-26T00:00:00Z","publist_id":"6826","publication":" Journal of Statistical Mechanics: Theory and Experiment","abstract":[{"text":"The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region.","lang":"eng"}]},{"department":[{"_id":"BjHo"}],"quality_controlled":"1","publication_status":"published","publisher":"Cambridge University Press","main_file_link":[{"url":"https://arxiv.org/abs/1703.10484","open_access":"1"}],"volume":827,"type":"journal_article","oa_version":"Submitted Version","scopus_import":"1","date_created":"2018-12-11T11:48:42Z","abstract":[{"text":"In shear flows at transitional Reynolds numbers, localized patches of turbulence, known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev. Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds number. Combining slicing methods for continuous symmetry reduction with Poincaré sections for the first time in a shear flow setting, we compute and visualize the unstable manifold of the lower-branch solution and show that it extends towards the neighbourhood of the upper-branch solution. Surprisingly, this connection even persists far above the bifurcation point and appears to mediate the first stage of the puff generation: amplification of streamwise localized fluctuations. When the state-space trajectories on the unstable manifold reach the vicinity of the upper branch, corresponding fluctuations expand in space and eventually take the usual shape of a puff.","lang":"eng"}],"status":"public","date_published":"2017-08-18T00:00:00Z","publication":"Journal of Fluid Mechanics","publist_id":"6824","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"       827","title":"Heteroclinic path to spatially localized chaos in pipe flow","doi":"10.1017/jfm.2017.516","isi":1,"external_id":{"isi":["000408326300001"]},"publication_identifier":{"issn":["00221120"]},"day":"18","date_updated":"2023-09-26T16:17:43Z","year":"2017","oa":1,"article_processing_charge":"No","month":"08","article_number":"R1","author":[{"first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"citation":{"mla":"Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 827, R1, Cambridge University Press, 2017, doi:<a href=\"https://doi.org/10.1017/jfm.2017.516\">10.1017/jfm.2017.516</a>.","short":"N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017).","chicago":"Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jfm.2017.516\">https://doi.org/10.1017/jfm.2017.516</a>.","ieee":"N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos in pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 827. Cambridge University Press, 2017.","ista":"Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 827, R1.","apa":"Budanur, N. B., &#38; Hof, B. (2017). Heteroclinic path to spatially localized chaos in pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.516\">https://doi.org/10.1017/jfm.2017.516</a>","ama":"Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow. <i>Journal of Fluid Mechanics</i>. 2017;827. doi:<a href=\"https://doi.org/10.1017/jfm.2017.516\">10.1017/jfm.2017.516</a>"},"_id":"824","language":[{"iso":"eng"}]},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02045"}],"volume":10424,"type":"conference","department":[{"_id":"HeEd"}],"editor":[{"full_name":"Felsberg, Michael","first_name":"Michael","last_name":"Felsberg"},{"full_name":"Heyden, Anders","first_name":"Anders","last_name":"Heyden"},{"full_name":"Krüger, Norbert","last_name":"Krüger","first_name":"Norbert"}],"quality_controlled":"1","publication_status":"published","publisher":"Springer","abstract":[{"text":"We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams.","lang":"eng"}],"date_published":"2017-07-28T00:00:00Z","status":"public","publist_id":"6815","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"     10424","oa_version":"Submitted Version","alternative_title":["LNCS"],"scopus_import":"1","date_created":"2018-12-11T11:48:45Z","conference":{"start_date":"2017-08-22","end_date":"2017-08-24","location":"Ystad, Sweden","name":"CAIP: Computer Analysis of Images and Patterns"},"year":"2017","oa":1,"article_processing_charge":"No","title":"Streaming algorithm for Euler characteristic curves of multidimensional images","doi":"10.1007/978-3-319-64689-3_32","isi":1,"external_id":{"isi":["000432085900032"]},"publication_identifier":{"issn":["03029743"]},"day":"28","date_updated":"2023-09-26T16:10:03Z","page":"397 - 409","language":[{"iso":"eng"}],"_id":"833","month":"07","author":[{"full_name":"Heiss, Teresa","orcid":"0000-0002-1780-2689","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","last_name":"Heiss","first_name":"Teresa"},{"id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Hubert","full_name":"Wagner, Hubert"}],"citation":{"short":"T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer, 2017, pp. 397–409.","mla":"Heiss, Teresa, and Hubert Wagner. <i>Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images</i>. Edited by Michael Felsberg et al., vol. 10424, Springer, 2017, pp. 397–409, doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>.","chicago":"Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden, and Norbert Krüger, 10424:397–409. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>.","ieee":"T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves of multidimensional images,” presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.","ista":"Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS, vol. 10424, 397–409.","apa":"Heiss, T., &#38; Wagner, H. (2017). Streaming algorithm for Euler characteristic curves of multidimensional images. In M. Felsberg, A. Heyden, &#38; N. Krüger (Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>","ama":"Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer; 2017:397-409. doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>"}},{"scopus_import":"1","date_created":"2018-12-11T11:48:45Z","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        96","abstract":[{"lang":"eng","text":"Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition."}],"publist_id":"6814","publication":"Physical Review B - Condensed Matter and Materials Physics","status":"public","date_published":"2017-09-06T00:00:00Z","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"quality_controlled":"1","type":"journal_article","volume":96,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02389"}],"citation":{"ista":"Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 96(10), 104201.","apa":"Serbyn, M., Zlatko, P., &#38; Abanin, D. (2017). Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>","ama":"Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2017;96(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>","mla":"Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>.","short":"M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017).","chicago":"Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>.","ieee":"M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 96, no. 10. American Physical Society, 2017."},"author":[{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zlatko, Papic","first_name":"Papic","last_name":"Zlatko"},{"full_name":"Abanin, Dmitry","last_name":"Abanin","first_name":"Dmitry"}],"month":"09","article_number":"104201","_id":"834","language":[{"iso":"eng"}],"acknowledgement":"We   acknowledge   useful   discussions with V. Kravtsov, T. Grover, and R. Vasseur.  M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4307.  M.S. and D.A.  acknowledge  hospitality  of  KITP,  where  parts  of this work were completed (supported in part by the National Science Foundation under Grant No. NSF PHY11-25915)","issue":"10","day":"06","publication_identifier":{"issn":["24699950"]},"date_updated":"2023-09-26T15:51:54Z","doi":"10.1103/PhysRevB.96.104201","title":"Thouless energy and multifractality across the many-body localization transition","external_id":{"isi":["000409429300004"]},"isi":1,"article_processing_charge":"No","oa":1,"year":"2017"},{"page":"119 - 136","_id":"836","language":[{"iso":"eng"}],"author":[{"full_name":"Ethier, Marc","last_name":"Ethier","first_name":"Marc"},{"full_name":"Jablonski, Grzegorz","orcid":"0000-0002-3536-9866","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","first_name":"Grzegorz","last_name":"Jablonski"},{"full_name":"Mrozek, Marian","last_name":"Mrozek","first_name":"Marian"}],"month":"07","citation":{"chicago":"Ethier, Marc, Grzegorz Jablonski, and Marian Mrozek. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” In <i>Special Sessions in Applications of Computer Algebra</i>, 198:119–36. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">https://doi.org/10.1007/978-3-319-56932-1_8</a>.","ieee":"M. Ethier, G. Jablonski, and M. Mrozek, “Finding eigenvalues of self-maps with the Kronecker canonical form,” in <i>Special Sessions in Applications of Computer Algebra</i>, Kalamata, Greece, 2017, vol. 198, pp. 119–136.","short":"M. Ethier, G. Jablonski, M. Mrozek, in:, Special Sessions in Applications of Computer Algebra, Springer, 2017, pp. 119–136.","mla":"Ethier, Marc, et al. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” <i>Special Sessions in Applications of Computer Algebra</i>, vol. 198, Springer, 2017, pp. 119–36, doi:<a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">10.1007/978-3-319-56932-1_8</a>.","ama":"Ethier M, Jablonski G, Mrozek M. Finding eigenvalues of self-maps with the Kronecker canonical form. In: <i>Special Sessions in Applications of Computer Algebra</i>. Vol 198. Springer; 2017:119-136. doi:<a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">10.1007/978-3-319-56932-1_8</a>","ista":"Ethier M, Jablonski G, Mrozek M. 2017. Finding eigenvalues of self-maps with the Kronecker canonical form. Special Sessions in Applications of Computer Algebra. ACA: Applications of Computer Algebra, PROMS, vol. 198, 119–136.","apa":"Ethier, M., Jablonski, G., &#38; Mrozek, M. (2017). Finding eigenvalues of self-maps with the Kronecker canonical form. In <i>Special Sessions in Applications of Computer Algebra</i> (Vol. 198, pp. 119–136). Kalamata, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">https://doi.org/10.1007/978-3-319-56932-1_8</a>"},"conference":{"end_date":"2015-07-23","start_date":"2015-07-20","name":"ACA: Applications of Computer Algebra","location":"Kalamata, Greece"},"ec_funded":1,"year":"2017","article_processing_charge":"No","doi":"10.1007/978-3-319-56932-1_8","title":"Finding eigenvalues of self-maps with the Kronecker canonical form","external_id":{"isi":["000434088200008"]},"isi":1,"day":"27","publication_identifier":{"isbn":["978-331956930-7"]},"date_updated":"2023-09-26T15:50:52Z","abstract":[{"text":"Recent research has examined how to study the topological features of a continuous self-map by means of the persistence of the eigenspaces, for given eigenvalues, of the endomorphism induced in homology over a field. This raised the question of how to select dynamically significant eigenvalues. The present paper aims to answer this question, giving an algorithm that computes the persistence of eigenspaces for every eigenvalue simultaneously, also expressing said eigenspaces as direct sums of “finite” and “singular” subspaces.","lang":"eng"}],"publist_id":"6812","publication":"Special Sessions in Applications of Computer Algebra","status":"public","date_published":"2017-07-27T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"       198","oa_version":"None","scopus_import":"1","alternative_title":["PROMS"],"date_created":"2018-12-11T11:48:46Z","type":"conference","volume":198,"department":[{"_id":"HeEd"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publisher":"Springer"},{"type":"dissertation","department":[{"_id":"JoCs"}],"supervisor":[{"last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. "}],"status":"public","date_published":"2017-08-23T00:00:00Z","publist_id":"6811","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:48:46Z","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"5828"}]},"year":"2017","oa":1,"article_processing_charge":"No","title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","doi":"10.15479/AT:ISTA:th_858","publication_identifier":{"issn":["2663-337X"]},"day":"23","date_updated":"2023-09-07T12:06:38Z","page":"93","degree_awarded":"PhD","acknowledgement":"I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ","_id":"837","pubrep_id":"858","language":[{"iso":"eng"}],"month":"08","file_date_updated":"2020-07-14T12:48:12Z","author":[{"id":"310349D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xu","first_name":"Haibing","full_name":"Xu, Haibing"}],"file":[{"access_level":"closed","date_created":"2019-04-05T08:59:51Z","date_updated":"2020-07-14T12:48:12Z","file_size":3589490,"file_id":"6213","file_name":"2017_Xu_Haibing_Thesis_Source.docx","relation":"source_file","creator":"dernst","checksum":"f11925fbbce31e495124b6bc4f10573c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_size":11668613,"file_id":"6214","access_level":"open_access","date_updated":"2020-07-14T12:48:12Z","date_created":"2019-04-05T08:59:51Z","content_type":"application/pdf","relation":"main_file","file_name":"2017_Xu_Thesis_IST.pdf","checksum":"ffb10749a537d615fab1ef0937ccb157","creator":"dernst"}],"citation":{"short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017.","mla":"Xu, Haibing. <i>Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>.","chicago":"Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>.","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","apa":"Xu, H. (2017). <i>Reactivation of the hippocampal cognitive map in goal-directed spatial tasks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>","ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>"},"ddc":["571"]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k &gt; 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. "}],"date_published":"2017-06-26T00:00:00Z","status":"public","publist_id":"6810","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:48:46Z","oa_version":"Published Version","type":"dissertation","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrPi"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"_id":"838","pubrep_id":"828","page":"86","citation":{"chicago":"Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>.","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","mla":"Rybar, Michal. <i>(The Exact Security of) Message Authentication Codes</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>.","short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017.","ama":"Rybar M. (The exact security of) Message authentication codes. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","apa":"Rybar, M. (2017). <i>(The exact security of) Message authentication codes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>"},"ddc":["000"],"file_date_updated":"2020-07-14T12:48:12Z","month":"06","author":[{"full_name":"Rybar, Michal","first_name":"Michal","last_name":"Rybar","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87"}],"file":[{"creator":"system","checksum":"ff8639ec4bded6186f44c7bd3ee26804","file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:10:13Z","date_updated":"2020-07-14T12:48:12Z","access_level":"open_access","file_id":"4799","file_size":847400},{"content_type":"application/zip","creator":"dernst","checksum":"3462101745ce8ad199c2d0f75dae4a7e","relation":"source_file","file_name":"2017_Thesis_Rybar_source.zip","file_id":"6202","file_size":26054879,"date_created":"2019-04-05T08:24:11Z","date_updated":"2020-07-14T12:48:12Z","access_level":"closed"}],"article_processing_charge":"No","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"2082","status":"public"},{"id":"6196","relation":"part_of_dissertation","status":"public"}]},"has_accepted_license":"1","year":"2017","publication_identifier":{"issn":["2663-337X"]},"day":"26","date_updated":"2023-09-07T12:02:28Z","title":"(The exact security of) Message authentication codes","doi":"10.15479/AT:ISTA:th_828"}]