[{"abstract":[{"text":"N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism.","lang":"eng"}],"article_number":"e2020857118","year":"2021","citation":{"short":"L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer, L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, PNAS 118 (2021).","chicago":"Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>PNAS</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>.","apa":"Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer, C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>","mla":"Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>PNAS</i>, vol. 118, no. 1, e2020857118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>.","ama":"Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>PNAS</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>","ieee":"L. Abas <i>et al.</i>, “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” <i>PNAS</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","ista":"Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. 118(1), e2020857118."},"_id":"8993","date_created":"2021-01-03T23:01:23Z","article_type":"original","acknowledgement":"This work was supported by Austrian Science Fund Grant FWF P21533-B20 (to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing access to mass spectrometry instruments at the Vienna BioCenter Core Facilities. We thank PNAS reviewers for the many comments and suggestions that helped to improve this manuscript.","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"doi":"10.1073/pnas.2020857118","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2020857118"}],"scopus_import":"1","article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","title":"Naphthylphthalamic acid associates with and inhibits PIN auxin transporters","intvolume":"       118","publication":"PNAS","date_updated":"2023-08-07T13:29:23Z","ec_funded":1,"department":[{"_id":"JiFr"},{"_id":"LeSa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Lindy","last_name":"Abas","full_name":"Abas, Lindy"},{"last_name":"Kolb","first_name":"Martina","full_name":"Kolb, Martina"},{"full_name":"Stadlmann, Johannes","last_name":"Stadlmann","first_name":"Johannes"},{"last_name":"Janacek","first_name":"Dorina P.","full_name":"Janacek, Dorina P."},{"last_name":"Lukic","first_name":"Kristina","full_name":"Lukic, Kristina","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1581-881X"},{"full_name":"Schwechheimer, Claus","first_name":"Claus","last_name":"Schwechheimer"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov"},{"first_name":"Lukas","last_name":"Mach","full_name":"Mach, Lukas"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Hammes, Ulrich Z.","first_name":"Ulrich Z.","last_name":"Hammes"}],"oa":1,"related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.2102232118","relation":"erratum"}]},"volume":118,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"}],"issue":"1","day":"05","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","month":"01","isi":1,"publisher":"National Academy of Sciences","pmid":1,"external_id":{"isi":["000607270100073"],"pmid":["33443187"]},"date_published":"2021-01-05T00:00:00Z","type":"journal_article"},{"abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"citation":{"ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” <i>PLOS Computational Biology</i>, vol. 17. Public Library of Science, 2021.","ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. 2021;17. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>","mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>, vol. 17, e1008529, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>.","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>."},"article_number":"e1008529","year":"2021","date_created":"2021-01-08T07:16:18Z","file":[{"file_id":"9092","creator":"dernst","content_type":"application/pdf","checksum":"e29f2b42651bef8e034781de8781ffac","access_level":"open_access","success":1,"file_name":"2021_PlosComBio_Kavcic.pdf","file_size":3690053,"relation":"main_file","date_created":"2021-02-04T12:30:48Z","date_updated":"2021-02-04T12:30:48Z"}],"_id":"8997","acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). ","publication_identifier":{"issn":["1553-7358"]},"article_type":"original","doi":"10.1371/journal.pcbi.1008529","article_processing_charge":"Yes","oa_version":"Published Version","file_date_updated":"2021-02-04T12:30:48Z","title":"Minimal biophysical model of combined antibiotic action","publication_status":"published","intvolume":"        17","date_updated":"2024-02-21T12:41:41Z","publication":"PLOS Computational Biology","department":[{"_id":"GaTk"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","first_name":"Tobias","last_name":"Bollenbach"}],"volume":17,"oa":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"7673"},{"status":"public","relation":"research_data","id":"8930"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","call_identifier":"FWF"},{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27"}],"has_accepted_license":"1","day":"07","quality_controlled":"1","keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"ddc":["570"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"01","publisher":"Public Library of Science","type":"journal_article","date_published":"2021-01-07T00:00:00Z","external_id":{"isi":["000608045000010"]}},{"doi":"10.3390/e23010058","scopus_import":"1","article_type":"original","acknowledgement":"This research was funded by the Central Research Development Fund of the University of\r\nBremen grant number ZF04B /2019/FB04 Avila_Kerstin (“Independent Project for Postdocs”). Shreyas Jalikop is acknowledged for recording some of the lifetime measurements\r\n","publication_identifier":{"eissn":["1099-4300"]},"publication_status":"published","title":"Second-order phase transition in counter-rotating taylor-couette flow experiment","file_date_updated":"2021-01-11T07:50:32Z","article_processing_charge":"No","oa_version":"Published Version","year":"2021","article_number":"58","citation":{"mla":"Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating Taylor-Couette Flow Experiment.” <i>Entropy</i>, vol. 23, no. 1, 58, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/e23010058\">10.3390/e23010058</a>.","chicago":"Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating Taylor-Couette Flow Experiment.” <i>Entropy</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/e23010058\">https://doi.org/10.3390/e23010058</a>.","short":"K. Avila, B. Hof, Entropy 23 (2021).","apa":"Avila, K., &#38; Hof, B. (2021). Second-order phase transition in counter-rotating taylor-couette flow experiment. <i>Entropy</i>. MDPI. <a href=\"https://doi.org/10.3390/e23010058\">https://doi.org/10.3390/e23010058</a>","ama":"Avila K, Hof B. Second-order phase transition in counter-rotating taylor-couette flow experiment. <i>Entropy</i>. 2021;23(1). doi:<a href=\"https://doi.org/10.3390/e23010058\">10.3390/e23010058</a>","ieee":"K. Avila and B. Hof, “Second-order phase transition in counter-rotating taylor-couette flow experiment,” <i>Entropy</i>, vol. 23, no. 1. MDPI, 2021.","ista":"Avila K, Hof B. 2021. Second-order phase transition in counter-rotating taylor-couette flow experiment. Entropy. 23(1), 58."},"abstract":[{"lang":"eng","text":"In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not\r\narise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available. "}],"_id":"8999","file":[{"relation":"main_file","date_created":"2021-01-11T07:50:32Z","date_updated":"2021-01-11T07:50:32Z","file_size":9456389,"file_name":"2021_Entropy_Avila.pdf","success":1,"access_level":"open_access","checksum":"3ba3dd8b7eecff713b72c5e9ba30d626","content_type":"application/pdf","file_id":"9003","creator":"dernst"}],"date_created":"2021-01-10T23:01:17Z","author":[{"first_name":"Kerstin","last_name":"Avila","id":"fcf74381-53e1-11eb-a6dc-b0e2acf78757","full_name":"Avila, Kerstin"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":23,"intvolume":"        23","department":[{"_id":"BjHo"}],"publication":"Entropy","date_updated":"2023-08-07T13:31:07Z","day":"01","quality_controlled":"1","issue":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publisher":"MDPI","pmid":1,"external_id":{"pmid":["33396499"],"isi":["000610135400001"]},"date_published":"2021-01-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"ddc":["530"],"month":"01","isi":1,"status":"public"},{"article_type":"original","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"doi":"10.1109/TIT.2020.3038806","scopus_import":"1","article_processing_charge":"No","oa_version":"Preprint","title":"Binary linear codes with optimal scaling: Polar codes with large kernels","publication_status":"published","abstract":[{"text":" We prove that, for the binary erasure channel (BEC), the polar-coding paradigm gives rise to codes that not only approach the Shannon limit but do so under the best possible scaling of their block length as a function of the gap to capacity. This result exhibits the first known family of binary codes that attain both optimal scaling and quasi-linear complexity of encoding and decoding. Our proof is based on the construction and analysis of binary polar codes with large kernels. When communicating reliably at rates within ε>0 of capacity, the code length n often scales as O(1/εμ), where the constant μ is called the scaling exponent. It is known that the optimal scaling exponent is μ=2, and it is achieved by random linear codes. The scaling exponent of conventional polar codes (based on the 2×2 kernel) on the BEC is μ=3.63. This falls far short of the optimal scaling guaranteed by random codes. Our main contribution is a rigorous proof of the following result: for the BEC, there exist ℓ×ℓ binary kernels, such that polar codes constructed from these kernels achieve scaling exponent μ(ℓ) that tends to the optimal value of 2 as ℓ grows. We furthermore characterize precisely how large ℓ needs to be as a function of the gap between μ(ℓ) and 2. The resulting binary codes maintain the recursive structure of conventional polar codes, and thereby achieve construction complexity O(n) and encoding/decoding complexity O(nlogn).","lang":"eng"}],"year":"2021","citation":{"chicago":"Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/TIT.2020.3038806\">https://doi.org/10.1109/TIT.2020.3038806</a>.","short":"A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, IEEE Transactions on Information Theory 67 (2021) 5693–5710.","apa":"Fazeli, A., Hassani, H., Mondelli, M., &#38; Vardy, A. (2021). Binary linear codes with optimal scaling: Polar codes with large kernels. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2020.3038806\">https://doi.org/10.1109/TIT.2020.3038806</a>","mla":"Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” <i>IEEE Transactions on Information Theory</i>, vol. 67, no. 9, IEEE, 2021, pp. 5693–710, doi:<a href=\"https://doi.org/10.1109/TIT.2020.3038806\">10.1109/TIT.2020.3038806</a>.","ieee":"A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with optimal scaling: Polar codes with large kernels,” <i>IEEE Transactions on Information Theory</i>, vol. 67, no. 9. IEEE, pp. 5693–5710, 2021.","ista":"Fazeli A, Hassani H, Mondelli M, Vardy A. 2021. Binary linear codes with optimal scaling: Polar codes with large kernels. IEEE Transactions on Information Theory. 67(9), 5693–5710.","ama":"Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal scaling: Polar codes with large kernels. <i>IEEE Transactions on Information Theory</i>. 2021;67(9):5693-5710. doi:<a href=\"https://doi.org/10.1109/TIT.2020.3038806\">10.1109/TIT.2020.3038806</a>"},"_id":"9002","date_created":"2021-01-10T23:01:18Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Fazeli","first_name":"Arman","full_name":"Fazeli, Arman"},{"full_name":"Hassani, Hamed","first_name":"Hamed","last_name":"Hassani"},{"first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"last_name":"Vardy","first_name":"Alexander","full_name":"Vardy, Alexander"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"6665"}]},"volume":67,"intvolume":"        67","arxiv":1,"publication":"IEEE Transactions on Information Theory","date_updated":"2024-03-07T12:18:50Z","department":[{"_id":"MaMo"}],"day":"01","page":"5693-5710","quality_controlled":"1","issue":"9","publisher":"IEEE","external_id":{"arxiv":["1711.01339"]},"date_published":"2021-09-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"status":"public","month":"09"},{"_id":"9005","date_created":"2021-01-17T23:01:10Z","abstract":[{"lang":"eng","text":"Studies on the experimental realization of two-dimensional anyons in terms of quasiparticles have been restricted, so far, to only anyons on the plane. It is known, however, that the geometry and topology of space can have significant effects on quantum statistics for particles moving on it. Here, we have undertaken the first step toward realizing the emerging fractional statistics for particles restricted to move on the sphere instead of on the plane. We show that such a model arises naturally in the context of quantum impurity problems. In particular, we demonstrate a setup in which the lowest-energy spectrum of two linear bosonic or fermionic molecules immersed in a quantum many-particle environment can coincide with the anyonic spectrum on the sphere. This paves the way toward the experimental realization of anyons on the sphere using molecular impurities. Furthermore, since a change in the alignment of the molecules corresponds to the exchange of the particles on the sphere, such a realization reveals a novel type of exclusion principle for molecular impurities, which could also be of use as a powerful technique to measure the statistics parameter. Finally, our approach opens up a simple numerical route to investigate the spectra of many anyons on the sphere. Accordingly, we present the spectrum of two anyons on the sphere in the presence of a Dirac monopole field."}],"article_number":"015301","year":"2021","citation":{"ieee":"M. Brooks, M. Lemeshko, D. Lundholm, and E. Yakaboylu, “Molecular impurities as a realization of anyons on the two-sphere,” <i>Physical Review Letters</i>, vol. 126, no. 1. American Physical Society, 2021.","ista":"Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. 2021. Molecular impurities as a realization of anyons on the two-sphere. Physical Review Letters. 126(1), 015301.","ama":"Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. Molecular impurities as a realization of anyons on the two-sphere. <i>Physical Review Letters</i>. 2021;126(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">10.1103/PhysRevLett.126.015301</a>","chicago":"Brooks, Morris, Mikhail Lemeshko, D. Lundholm, and Enderalp Yakaboylu. “Molecular Impurities as a Realization of Anyons on the Two-Sphere.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">https://doi.org/10.1103/PhysRevLett.126.015301</a>.","apa":"Brooks, M., Lemeshko, M., Lundholm, D., &#38; Yakaboylu, E. (2021). Molecular impurities as a realization of anyons on the two-sphere. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">https://doi.org/10.1103/PhysRevLett.126.015301</a>","short":"M. Brooks, M. Lemeshko, D. Lundholm, E. Yakaboylu, Physical Review Letters 126 (2021).","mla":"Brooks, Morris, et al. “Molecular Impurities as a Realization of Anyons on the Two-Sphere.” <i>Physical Review Letters</i>, vol. 126, no. 1, 015301, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">10.1103/PhysRevLett.126.015301</a>."},"oa_version":"Preprint","article_processing_charge":"No","title":"Molecular impurities as a realization of anyons on the two-sphere","publication_status":"published","article_type":"original","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"acknowledgement":"We are grateful to A. Ghazaryan for valuable discussions and also thank the anonymous referees for comments. D.L. acknowledges financial support from the G¨oran Gustafsson Foundation (grant no. 1804) and LMU Munich. M.L. gratefully acknowledges financial support\r\nby the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 801770).","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.05948"}],"doi":"10.1103/PhysRevLett.126.015301","scopus_import":"1","publication":"Physical Review Letters","ec_funded":1,"date_updated":"2023-08-07T13:32:10Z","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"intvolume":"       126","arxiv":1,"oa":1,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/dancing-molecules-and-two-dimensional-particles/"}],"record":[{"relation":"dissertation_contains","status":"public","id":"12390"}]},"volume":126,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Brooks","first_name":"Morris","full_name":"Brooks, Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","orcid":"0000-0002-6249-0928"},{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"D.","last_name":"Lundholm","full_name":"Lundholm, D."},{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","last_name":"Yakaboylu","first_name":"Enderalp"}],"project":[{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770"}],"issue":"1","quality_controlled":"1","day":"08","status":"public","month":"01","isi":1,"language":[{"iso":"eng"}],"date_published":"2021-01-08T00:00:00Z","external_id":{"isi":["000606325000003"],"arxiv":["2009.05948"]},"type":"journal_article","publisher":"American Physical Society"},{"article_type":"original","acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"doi":"10.1016/j.devcel.2020.12.002","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2020.12.002","open_access":"1"}],"scopus_import":"1","article_processing_charge":"No","oa_version":"Published Version","title":"Cytoplasm's got moves","publication_status":"published","abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species.","lang":"eng"}],"year":"2021","citation":{"mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>.","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>.","apa":"Shamipour, S., Caballero Mancebo, S., &#38; Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>","ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226.","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” <i>Developmental Cell</i>, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. <i>Developmental Cell</i>. 2021;56(2):P213-226. doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>"},"_id":"9006","date_created":"2021-01-17T23:01:10Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","first_name":"Shayan","last_name":"Shamipour"},{"first_name":"Silvia","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"oa":1,"related_material":{"record":[{"id":"9623","relation":"dissertation_contains","status":"public"}]},"volume":56,"intvolume":"        56","publication":"Developmental Cell","date_updated":"2024-03-25T23:30:10Z","department":[{"_id":"CaHe"}],"day":"25","page":"P213-226","quality_controlled":"1","issue":"2","publisher":"Elsevier","pmid":1,"external_id":{"isi":["000613273900009"],"pmid":["33321104"]},"date_published":"2021-01-25T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"status":"public","month":"01","isi":1},{"article_type":"original","acknowledgement":"This work was supported by National Institute of Health grants R01 EY030123, P30 EY016665, and T32 GM081061, an unrestricted research grant from Research to Prevent Blindness, Inc., and the Frederick A. Davis Endowment from the Department of Ophthalmology and Visual Sciences at the University of Wisconsin-Madison.","publication_identifier":{"issn":["1360-8185"],"eissn":["1573-675X"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082518/","open_access":"1"}],"doi":"10.1007/s10495-020-01654-w","scopus_import":"1","article_processing_charge":"No","oa_version":"Submitted Version","title":"Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis","publication_status":"published","abstract":[{"text":"Recent advancements in live cell imaging technologies have identified the phenomenon of intracellular propagation of late apoptotic events, such as cytochrome c release and caspase activation. The mechanism, prevalence, and speed of apoptosis propagation remain unclear. Additionally, no studies have demonstrated propagation of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome c and SMAC/Diablo release and is affected by cellular morphology, such that cells with processes are more likely to exhibit propagation. The initiation of propagation events is most prevalent in the distal tips of processes, while the rate of propagation is influenced by the 2-dimensional width of the process. Propagation was rarely observed in the cell soma, which exhibited near synchronous recruitment of BAX. Propagation velocity is not affected by mitochondrial volume in segments of processes, but is negatively affected by mitochondrial density. There was no evidence of a propagating wave of increased levels of intracellular calcium ions. Alternatively, we did observe a uniform increase in superoxide build-up in cellular mitochondria, which was released as a propagating wave simultaneously with the propagating recruitment of BAX to the mitochondrial outer membrane.","lang":"eng"}],"year":"2021","citation":{"short":"J.A. Grosser, M.E. Maes, R.W. Nickells, Apoptosis 26 (2021) 132–145.","apa":"Grosser, J. A., Maes, M. E., &#38; Nickells, R. W. (2021). Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. <i>Apoptosis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10495-020-01654-w\">https://doi.org/10.1007/s10495-020-01654-w</a>","chicago":"Grosser, Joshua A., Margaret E Maes, and Robert W. Nickells. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” <i>Apoptosis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s10495-020-01654-w\">https://doi.org/10.1007/s10495-020-01654-w</a>.","mla":"Grosser, Joshua A., et al. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” <i>Apoptosis</i>, vol. 26, no. 2, Springer Nature, 2021, pp. 132–45, doi:<a href=\"https://doi.org/10.1007/s10495-020-01654-w\">10.1007/s10495-020-01654-w</a>.","ieee":"J. A. Grosser, M. E. Maes, and R. W. Nickells, “Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis,” <i>Apoptosis</i>, vol. 26, no. 2. Springer Nature, pp. 132–145, 2021.","ista":"Grosser JA, Maes ME, Nickells RW. 2021. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. Apoptosis. 26(2), 132–145.","ama":"Grosser JA, Maes ME, Nickells RW. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. <i>Apoptosis</i>. 2021;26(2):132-145. doi:<a href=\"https://doi.org/10.1007/s10495-020-01654-w\">10.1007/s10495-020-01654-w</a>"},"_id":"9009","date_created":"2021-01-17T23:01:11Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Grosser, Joshua A.","last_name":"Grosser","first_name":"Joshua A."},{"last_name":"Maes","first_name":"Margaret E","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nickells, Robert W.","last_name":"Nickells","first_name":"Robert W."}],"oa":1,"volume":26,"intvolume":"        26","publication":"Apoptosis","date_updated":"2023-08-07T13:32:40Z","department":[{"_id":"SaSi"}],"day":"01","page":"132-145","quality_controlled":"1","issue":"2","publisher":"Springer Nature","pmid":1,"external_id":{"isi":["000606722600001"],"pmid":["33426618"]},"date_published":"2021-02-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"status":"public","month":"02","isi":1},{"acknowledged_ssus":[{"_id":"Bio"}],"volume":40,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"id":"10303","status":"public","relation":"dissertation_contains"}]},"oa":1,"author":[{"first_name":"Krisztina","last_name":"Ötvös","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","full_name":"Ötvös, Krisztina"},{"first_name":"Marco","last_name":"Marconi","full_name":"Marconi, Marco"},{"full_name":"Vega, Andrea","first_name":"Andrea","last_name":"Vega"},{"last_name":"O’Brien","first_name":"Jose","full_name":"O’Brien, Jose"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J"},{"first_name":"Rashed","last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed"},{"first_name":"Livio","last_name":"Antonielli","full_name":"Antonielli, Livio"},{"full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","first_name":"Juan C"},{"first_name":"Yuzhou","last_name":"Zhang","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou"},{"first_name":"Shutang","last_name":"Tan","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"first_name":"Candela","last_name":"Cuesta","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela"},{"first_name":"Christina","last_name":"Artner","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","full_name":"Artner, Christina"},{"full_name":"Bouguyon, Eleonore","first_name":"Eleonore","last_name":"Bouguyon"},{"last_name":"Gojon","first_name":"Alain","full_name":"Gojon, Alain"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"},{"first_name":"Rodrigo A.","last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A."},{"full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","last_name":"Wabnik","first_name":"Krzysztof T"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"date_updated":"2024-03-25T23:30:22Z","publication":"EMBO Journal","intvolume":"        40","publication_status":"published","title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","file_date_updated":"2021-02-11T12:28:29Z","scopus_import":"1","doi":"10.15252/embj.2020106862","publication_identifier":{"eissn":["14602075"],"issn":["02614189"]},"acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","article_type":"original","file":[{"checksum":"dc55c900f3b061d6c2790b8813d759a3","content_type":"application/pdf","creator":"dernst","file_id":"9110","file_size":2358617,"relation":"main_file","date_created":"2021-02-11T12:28:29Z","date_updated":"2021-02-11T12:28:29Z","success":1,"access_level":"open_access","file_name":"2021_Embo_Otvos.pdf"}],"date_created":"2021-01-17T23:01:12Z","_id":"9010","citation":{"mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>, vol. 40, no. 3, e106862, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>.","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>","chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>.","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. 2021;40(3). doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862.","ieee":"K. Ötvös <i>et al.</i>, “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” <i>EMBO Journal</i>, vol. 40, no. 3. Embo Press, 2021."},"year":"2021","article_number":"e106862","abstract":[{"text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.","lang":"eng"}],"type":"journal_article","external_id":{"isi":["000604645600001"],"pmid":[" 33399250"]},"date_published":"2021-02-01T00:00:00Z","pmid":1,"publisher":"Embo Press","isi":1,"month":"02","status":"public","ddc":["580"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"01","issue":"3","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I 1774-B16"},{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"},{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0001-6814-7541","id":"1083E038-9F73-11E9-A4B5-532AE6697425","full_name":"Gulden, Tobias","first_name":"Tobias","last_name":"Gulden"},{"full_name":"Kamenev, Alex","first_name":"Alex","last_name":"Kamenev"}],"volume":23,"oa":1,"intvolume":"        23","arxiv":1,"date_updated":"2023-08-07T13:34:18Z","ec_funded":1,"publication":"Entropy","department":[{"_id":"MaSe"}],"publication_identifier":{"eissn":["1099-4300"]},"acknowledgement":"A.K. was supported by NSF grants DMR-2037654. T.G. acknowledges funding from the Institute of Science and Technology (IST) Austria, and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411.\r\nWe are indebted to Boris Shklovskii for introducing us to the problem, and Alexander Gorsky and Peter Koroteev for introducing us to the Picard-Fuchs methods. A very special thanks goes to Michael Janas for several years of excellent collaboration on these topics. TG thanks Michael Kreshchuk for introduction to the exact WKB method and great collaboration on related projects. Figure 3 and Figure 4 are reproduced from Reference [25] with friendly permission by the Russian Academy of Sciences. Figure 2, Figure 4, Figure 5, Figure 6, and Figure 8 are reproduced from Reference [26] with friendly permission by IOP Publishing.","article_type":"original","doi":"10.3390/e23010125","oa_version":"Published Version","article_processing_charge":"Yes","file_date_updated":"2021-01-19T11:11:14Z","publication_status":"published","title":"Dynamics of ion channels via non-hermitian quantum mechanics","abstract":[{"lang":"eng","text":"We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels. "}],"citation":{"ama":"Gulden T, Kamenev A. Dynamics of ion channels via non-hermitian quantum mechanics. <i>Entropy</i>. 2021;23(1). doi:<a href=\"https://doi.org/10.3390/e23010125\">10.3390/e23010125</a>","ieee":"T. Gulden and A. Kamenev, “Dynamics of ion channels via non-hermitian quantum mechanics,” <i>Entropy</i>, vol. 23, no. 1. MDPI, 2021.","ista":"Gulden T, Kamenev A. 2021. Dynamics of ion channels via non-hermitian quantum mechanics. Entropy. 23(1), e23010125.","short":"T. Gulden, A. Kamenev, Entropy 23 (2021).","apa":"Gulden, T., &#38; Kamenev, A. (2021). Dynamics of ion channels via non-hermitian quantum mechanics. <i>Entropy</i>. MDPI. <a href=\"https://doi.org/10.3390/e23010125\">https://doi.org/10.3390/e23010125</a>","chicago":"Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” <i>Entropy</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/e23010125\">https://doi.org/10.3390/e23010125</a>.","mla":"Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” <i>Entropy</i>, vol. 23, no. 1, e23010125, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/e23010125\">10.3390/e23010125</a>."},"article_number":"e23010125","year":"2021","date_created":"2021-01-19T11:12:06Z","file":[{"access_level":"open_access","file_name":"Final published paper.pdf","date_updated":"2021-01-19T11:11:14Z","date_created":"2021-01-19T11:11:14Z","file_size":981285,"relation":"main_file","creator":"tgulden","file_id":"9021","content_type":"application/pdf","checksum":"6cd0e706156827c45c740534bd32c179"}],"_id":"9020","publisher":"MDPI","type":"journal_article","external_id":{"arxiv":["2012.01390"],"isi":["000610122000001"]},"date_published":"2021-01-19T00:00:00Z","ddc":["530"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"01","day":"19","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"has_accepted_license":"1","issue":"1"},{"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Giorgio","last_name":"Cipolloni","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio"}],"date_updated":"2023-09-07T13:29:32Z","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"LaEr"}],"degree_awarded":"PhD","file_date_updated":"2021-01-25T14:19:10Z","article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","title":"Fluctuations in the spectrum of random matrices","acknowledgement":"I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:9022","_id":"9022","date_created":"2021-01-21T18:16:54Z","file":[{"checksum":"5a93658a5f19478372523ee232887e2b","content_type":"application/pdf","creator":"gcipollo","file_id":"9043","date_updated":"2021-01-25T14:19:03Z","relation":"main_file","date_created":"2021-01-25T14:19:03Z","file_size":4127796,"access_level":"open_access","success":1,"file_name":"thesis.pdf"},{"file_name":"Thesis_files.zip","access_level":"closed","date_updated":"2021-01-25T14:19:10Z","file_size":12775206,"date_created":"2021-01-25T14:19:10Z","relation":"source_file","content_type":"application/zip","creator":"gcipollo","file_id":"9044","checksum":"e8270eddfe6a988e92a53c88d1d19b8c"}],"abstract":[{"text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices.","lang":"eng"}],"supervisor":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","last_name":"Erdös"}],"year":"2021","citation":{"mla":"Cipolloni, Giorgio. <i>Fluctuations in the Spectrum of Random Matrices</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9022\">10.15479/AT:ISTA:9022</a>.","chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9022\">https://doi.org/10.15479/AT:ISTA:9022</a>.","short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","apa":"Cipolloni, G. (2021). <i>Fluctuations in the spectrum of random matrices</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9022\">https://doi.org/10.15479/AT:ISTA:9022</a>","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria.","ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9022\">10.15479/AT:ISTA:9022</a>"},"date_published":"2021-01-25T00:00:00Z","type":"dissertation","publisher":"Institute of Science and Technology Austria","status":"public","month":"01","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"ddc":["510"],"day":"25","page":"380","project":[{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7"}],"has_accepted_license":"1"},{"arxiv":1,"intvolume":"       380","department":[{"_id":"LaEr"}],"date_updated":"2023-08-07T13:34:48Z","ec_funded":1,"publication":"Advances in Mathematics","author":[{"first_name":"Daniel","last_name":"Virosztek","orcid":"0000-0003-1109-5511","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","full_name":"Virosztek, Daniel"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":380,"oa":1,"citation":{"short":"D. Virosztek, Advances in Mathematics 380 (2021).","chicago":"Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” <i>Advances in Mathematics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.aim.2021.107595\">https://doi.org/10.1016/j.aim.2021.107595</a>.","apa":"Virosztek, D. (2021). The metric property of the quantum Jensen-Shannon divergence. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2021.107595\">https://doi.org/10.1016/j.aim.2021.107595</a>","mla":"Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” <i>Advances in Mathematics</i>, vol. 380, no. 3, 107595, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107595\">10.1016/j.aim.2021.107595</a>.","ista":"Virosztek D. 2021. The metric property of the quantum Jensen-Shannon divergence. Advances in Mathematics. 380(3), 107595.","ieee":"D. Virosztek, “The metric property of the quantum Jensen-Shannon divergence,” <i>Advances in Mathematics</i>, vol. 380, no. 3. Elsevier, 2021.","ama":"Virosztek D. The metric property of the quantum Jensen-Shannon divergence. <i>Advances in Mathematics</i>. 2021;380(3). doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107595\">10.1016/j.aim.2021.107595</a>"},"article_number":"107595","year":"2021","abstract":[{"text":"In this short note, we prove that the square root of the quantum Jensen-Shannon divergence is a true metric on the cone of positive matrices, and hence in particular on the quantum state space.","lang":"eng"}],"date_created":"2021-01-22T17:55:17Z","_id":"9036","doi":"10.1016/j.aim.2021.107595","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.10447"}],"acknowledgement":"D. Virosztek was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K124152, and no. KH129601.","publication_identifier":{"issn":["0001-8708"]},"article_type":"original","title":"The metric property of the quantum Jensen-Shannon divergence","publication_status":"published","article_processing_charge":"No","oa_version":"Preprint","language":[{"iso":"eng"}],"keyword":["General Mathematics"],"isi":1,"month":"03","status":"public","publisher":"Elsevier","type":"journal_article","external_id":{"arxiv":["1910.10447"],"isi":["000619676100035"]},"date_published":"2021-03-26T00:00:00Z","issue":"3","project":[{"_id":"26A455A6-B435-11E9-9278-68D0E5697425","name":"Geometric study of Wasserstein spaces and free probability","grant_number":"846294","call_identifier":"H2020"}],"day":"26","quality_controlled":"1"},{"publication":"Bulletin of the London Mathematical Society","date_updated":"2023-08-07T13:35:20Z","department":[{"_id":"UlWa"}],"intvolume":"        53","arxiv":1,"oa":1,"volume":53,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","last_name":"Ivanov","first_name":"Grigory"}],"_id":"9037","file":[{"access_level":"open_access","success":1,"file_name":"2021_BLMS_Ivanov.pdf","relation":"main_file","file_size":194550,"date_created":"2021-08-06T09:59:45Z","date_updated":"2021-08-06T09:59:45Z","file_id":"9796","creator":"kschuh","content_type":"application/pdf","checksum":"e6ceaa6470d835eb4c211cbdd38fdfd1"}],"date_created":"2021-01-24T23:01:08Z","abstract":[{"text":"We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial and convex geometry in Banach spaces. We generalize some results of the paper (Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego, California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg theorem, the selection lemma and the weak  𝜀 ‐net theorem in Banach spaces of type  𝑝>1 . To prove these results, we use the original ideas of Adiprasito, Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon theorem and slightly modified version of the celebrated Maurey lemma.","lang":"eng"}],"year":"2021","citation":{"short":"G. Ivanov, Bulletin of the London Mathematical Society 53 (2021) 631–641.","apa":"Ivanov, G. (2021). No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/blms.12449\">https://doi.org/10.1112/blms.12449</a>","chicago":"Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society, 2021. <a href=\"https://doi.org/10.1112/blms.12449\">https://doi.org/10.1112/blms.12449</a>.","mla":"Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2, London Mathematical Society, 2021, pp. 631–41, doi:<a href=\"https://doi.org/10.1112/blms.12449\">10.1112/blms.12449</a>.","ama":"Ivanov G. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. <i>Bulletin of the London Mathematical Society</i>. 2021;53(2):631-641. doi:<a href=\"https://doi.org/10.1112/blms.12449\">10.1112/blms.12449</a>","ieee":"G. Ivanov, “No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p,” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2. London Mathematical Society, pp. 631–641, 2021.","ista":"Ivanov G. 2021. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. Bulletin of the London Mathematical Society. 53(2), 631–641."},"file_date_updated":"2021-08-06T09:59:45Z","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","title":"No-dimension Tverberg's theorem and its corollaries in Banach spaces of type p","publication_status":"published","article_type":"original","acknowledgement":"I wish to thank Imre Bárány for bringing the problem to my attention. I am grateful to Marton Naszódi and Igor Tsiutsiurupa for useful remarks and help with the text.\r\nThe author acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075‐15‐2019‐1926.","publication_identifier":{"eissn":["14692120"],"issn":["00246093"]},"doi":"10.1112/blms.12449","scopus_import":"1","status":"public","month":"04","isi":1,"language":[{"iso":"eng"}],"ddc":["510"],"external_id":{"isi":["000607265100001"],"arxiv":["1912.08561"]},"date_published":"2021-04-01T00:00:00Z","type":"journal_article","publisher":"London Mathematical Society","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"issue":"2","quality_controlled":"1","day":"01","page":"631-641"},{"doi":"10.1371/journal.ppat.1009172","scopus_import":"1","article_type":"original","publication_identifier":{"issn":["15537366"],"eissn":["15537374"]},"acknowledgement":"Our work was supported by the Swedish Research Council (grant 2017-01527) to DIA","title":"Mechanisms and therapeutic potential of collateral sensitivity to antibiotics","publication_status":"published","file_date_updated":"2021-02-03T12:13:03Z","article_processing_charge":"No","oa_version":"Published Version","article_number":"e1009172","year":"2021","citation":{"apa":"Römhild, R., &#38; Andersson, D. I. (2021). Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1009172\">https://doi.org/10.1371/journal.ppat.1009172</a>","short":"R. Römhild, D.I. Andersson, PLoS Pathogens 17 (2021).","chicago":"Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” <i>PLoS Pathogens</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.ppat.1009172\">https://doi.org/10.1371/journal.ppat.1009172</a>.","mla":"Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” <i>PLoS Pathogens</i>, vol. 17, no. 1, e1009172, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1009172\">10.1371/journal.ppat.1009172</a>.","ama":"Römhild R, Andersson DI. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. <i>PLoS Pathogens</i>. 2021;17(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1009172\">10.1371/journal.ppat.1009172</a>","ista":"Römhild R, Andersson DI. 2021. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. PLoS Pathogens. 17(1), e1009172.","ieee":"R. Römhild and D. I. Andersson, “Mechanisms and therapeutic potential of collateral sensitivity to antibiotics,” <i>PLoS Pathogens</i>, vol. 17, no. 1. Public Library of Science, 2021."},"_id":"9046","file":[{"content_type":"application/pdf","file_id":"9070","creator":"dernst","checksum":"d745d7f8fcbb9b95fea16a36f94dee31","access_level":"open_access","success":1,"file_name":"2021_PlosPathogens_Roemhild.pdf","relation":"main_file","file_size":570066,"date_created":"2021-02-03T12:13:03Z","date_updated":"2021-02-03T12:13:03Z"}],"date_created":"2021-01-31T23:01:21Z","author":[{"full_name":"Römhild, Roderich","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","orcid":"0000-0001-9480-5261","last_name":"Römhild","first_name":"Roderich"},{"last_name":"Andersson","first_name":"Dan I.","full_name":"Andersson, Dan I."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":17,"intvolume":"        17","department":[{"_id":"CaGu"}],"publication":"PLoS Pathogens","date_updated":"2023-08-07T13:36:55Z","day":"14","quality_controlled":"1","issue":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","publisher":"Public Library of Science","pmid":1,"date_published":"2021-01-14T00:00:00Z","external_id":{"pmid":["33444399"],"isi":["000610190400007"]},"type":"journal_article","language":[{"iso":"eng"}],"ddc":["570"],"month":"01","isi":1,"status":"public"},{"issue":"1","day":"01","page":"18-27","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","month":"01","isi":1,"publisher":"IEEE","external_id":{"isi":["000607808800002"],"arxiv":["1909.04892"]},"date_published":"2021-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block length and μ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 or 1.","lang":"eng"}],"year":"2021","citation":{"ieee":"M. Mondelli, S. A. Hashemi, J. M. Cioffi, and A. Goldsmith, “Sublinear latency for simplified successive cancellation decoding of polar codes,” <i>IEEE Transactions on Wireless Communications</i>, vol. 20, no. 1. IEEE, pp. 18–27, 2021.","ista":"Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. 2021. Sublinear latency for simplified successive cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 20(1), 18–27.","ama":"Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. Sublinear latency for simplified successive cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. 2021;20(1):18-27. doi:<a href=\"https://doi.org/10.1109/TWC.2020.3022922\">10.1109/TWC.2020.3022922</a>","mla":"Mondelli, Marco, et al. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>, vol. 20, no. 1, IEEE, 2021, pp. 18–27, doi:<a href=\"https://doi.org/10.1109/TWC.2020.3022922\">10.1109/TWC.2020.3022922</a>.","short":"M. Mondelli, S.A. Hashemi, J.M. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 20 (2021) 18–27.","chicago":"Mondelli, Marco, Seyyed Ali Hashemi, John M. Cioffi, and Andrea Goldsmith. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/TWC.2020.3022922\">https://doi.org/10.1109/TWC.2020.3022922</a>.","apa":"Mondelli, M., Hashemi, S. A., Cioffi, J. M., &#38; Goldsmith, A. (2021). Sublinear latency for simplified successive cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/TWC.2020.3022922\">https://doi.org/10.1109/TWC.2020.3022922</a>"},"_id":"9047","date_created":"2021-01-31T23:01:21Z","article_type":"original","publication_identifier":{"issn":["15361276"],"eissn":["15582248"]},"acknowledgement":"M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305, IIS-1741162, and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei. The authors would like to thank the anonymous reviewers for their comments that helped improving the quality of the manuscript.","main_file_link":[{"url":"https://arxiv.org/abs/1909.04892","open_access":"1"}],"doi":"10.1109/TWC.2020.3022922","scopus_import":"1","article_processing_charge":"No","oa_version":"Preprint","publication_status":"published","title":"Sublinear latency for simplified successive cancellation decoding of polar codes","intvolume":"        20","arxiv":1,"publication":"IEEE Transactions on Wireless Communications","date_updated":"2023-08-07T13:36:25Z","department":[{"_id":"MaMo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi","first_name":"Seyyed Ali"},{"last_name":"Cioffi","first_name":"John M.","full_name":"Cioffi, John M."},{"full_name":"Goldsmith, Andrea","first_name":"Andrea","last_name":"Goldsmith"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"8536"}]},"oa":1,"volume":20},{"keyword":["General Physics and Astronomy"],"language":[{"iso":"eng"}],"ddc":["530"],"status":"public","month":"01","isi":1,"publisher":"American Physical Society","external_id":{"isi":["000613148200001"],"arxiv":["2008.04894"]},"date_published":"2021-01-29T00:00:00Z","type":"journal_article","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","issue":"4","day":"29","quality_controlled":"1","intvolume":"       126","arxiv":1,"publication":"Physical Review Letters","ec_funded":1,"date_updated":"2023-09-05T12:08:58Z","department":[{"_id":"MaSe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"De Nicola, Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4842-6671","last_name":"De Nicola","first_name":"Stefano"},{"full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym"}],"oa":1,"volume":126,"abstract":[{"text":"The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology.","lang":"eng"}],"article_number":"040602","year":"2021","citation":{"mla":"De Nicola, Stefano, et al. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>, vol. 126, no. 4, 040602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>.","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021).","apa":"De Nicola, S., Michailidis, A., &#38; Serbyn, M. (2021). Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>","chicago":"De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>.","ieee":"S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement view of dynamical quantum phase transitions,” <i>Physical Review Letters</i>, vol. 126, no. 4. American Physical Society, 2021.","ista":"De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 126(4), 040602.","ama":"De Nicola S, Michailidis A, Serbyn M. Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. 2021;126(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>"},"_id":"9048","file":[{"date_created":"2021-02-03T12:47:04Z","relation":"main_file","file_size":398075,"date_updated":"2021-02-03T12:47:04Z","access_level":"open_access","success":1,"file_name":"2021_PhysicalRevLett_DeNicola.pdf","checksum":"d9acbc502390ed7a97e631d23ae19ecd","creator":"dernst","file_id":"9074","content_type":"application/pdf"}],"date_created":"2021-02-01T09:20:00Z","article_type":"original","acknowledgement":"S. D. N. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. M. and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and\r\nInnovation Programme (Grant Agreement No. 850899).","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"doi":"10.1103/physrevlett.126.040602","file_date_updated":"2021-02-03T12:47:04Z","article_processing_charge":"Yes","oa_version":"Published Version","publication_status":"published","title":"Entanglement view of dynamical quantum phase transitions"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F"}],"oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"187"},{"id":"8703","status":"public","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","date_updated":"2023-09-07T13:29:01Z","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:9056","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2021-02-03T10:37:28Z","title":"Multi-cover persistence and Delaunay mosaics","publication_status":"published","abstract":[{"text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets.","lang":"eng"}],"supervisor":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner"}],"citation":{"mla":"Osang, Georg F. <i>Multi-Cover Persistence and Delaunay Mosaics</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9056\">10.15479/AT:ISTA:9056</a>.","short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021.","apa":"Osang, G. F. (2021). <i>Multi-cover persistence and Delaunay mosaics</i>. Institute of Science and Technology Austria, Klosterneuburg. <a href=\"https://doi.org/10.15479/AT:ISTA:9056\">https://doi.org/10.15479/AT:ISTA:9056</a>","chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9056\">https://doi.org/10.15479/AT:ISTA:9056</a>.","ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9056\">10.15479/AT:ISTA:9056</a>","ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021."},"place":"Klosterneuburg","year":"2021","date_created":"2021-02-02T14:11:06Z","file":[{"creator":"patrickd","file_id":"9063","content_type":"application/zip","checksum":"bcf27986147cab0533b6abadd74e7629","file_name":"thesis_source.zip","access_level":"closed","date_created":"2021-02-02T14:09:25Z","relation":"source_file","date_updated":"2021-02-03T10:37:28Z","file_size":13446994},{"date_created":"2021-02-02T14:09:18Z","relation":"main_file","file_size":5210329,"date_updated":"2021-02-02T14:09:18Z","file_name":"thesis_pdfA2b.pdf","access_level":"open_access","success":1,"checksum":"9cc8af266579a464385bbe2aff6af606","file_id":"9064","creator":"patrickd","content_type":"application/pdf"}],"_id":"9056","publisher":"Institute of Science and Technology Austria","type":"dissertation","date_published":"2021-02-01T00:00:00Z","alternative_title":["ISTA Thesis"],"ddc":["006","514","516"],"language":[{"iso":"eng"}],"status":"public","month":"02","day":"01","page":"134","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"}},{"quality_controlled":"1","day":"03","page":"813-822","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780"},{"grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"has_accepted_license":"1","issue":"5","external_id":{"pmid":["33431633"],"isi":["000616763400002"]},"date_published":"2021-02-03T00:00:00Z","type":"journal_article","publisher":"Society for Neuroscience","pmid":1,"status":"public","month":"02","isi":1,"keyword":["General Neuroscience"],"language":[{"iso":"eng"}],"ddc":["570"],"file_date_updated":"2022-05-27T06:59:55Z","oa_version":"Published Version","article_processing_charge":"No","title":"The logic of developing neocortical circuits in health and disease","publication_status":"published","article_type":"original","acknowledgement":"Work in the I.L.H.-O. laboratory was supported by European Research Council Grant ERC-2015-CoG 681577 and German Research Foundation Ha 4466/10-1, Ha4466/11-1, Ha4466/12-1, SPP 1665, and SFB 936B5. Work in the S.J.B.B. laboratory was supported by Biotechnology and Biological Sciences Research Council BB/P003796/1, Medical Research Council MR/K004387/1 and MR/T033320/1, Wellcome Trust 215199/Z/19/Z and 102386/Z/13/Z, and John Fell Fund. Work in the S.H. laboratory was supported by European Research Council Grants ERC-2016-CoG 725780 LinPro and FWF SFB F78. This work was supported by National Institutes of Health Grant NIMH 1R01MH110553 to N.V.D.M.G. Work in the J.A.C. laboratory was supported by the Ludwig Family Foundation, Simons Foundation SFARI Research Award, and National Institutes of Health/National Institute of Mental Health R01 MH102365 and R01MH113852. The B.V. laboratory was supported by Whitehall Foundation 2017-12-73, National Science Foundation 1736028, National Institutes of Health, National Institute of General Medical Sciences R01GM134363-01, and Halıcıoğlu Data Science Institute Fellowship. This work was supported by the University of California San Diego School of Medicine.","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"doi":"10.1523/jneurosci.1655-20.2020","scopus_import":"1","_id":"9073","file":[{"file_name":"2021_JourNeuroscience_Hanganu.pdf","success":1,"access_level":"open_access","date_updated":"2022-05-27T06:59:55Z","date_created":"2022-05-27T06:59:55Z","relation":"main_file","file_size":1031150,"file_id":"11414","creator":"dernst","content_type":"application/pdf","checksum":"578fd7ed1a0aef74bce61bea2d987b33"}],"date_created":"2021-02-03T12:23:51Z","abstract":[{"text":"The sensory and cognitive abilities of the mammalian neocortex are underpinned by intricate columnar and laminar circuits formed from an array of diverse neuronal populations. One approach to determining how interactions between these circuit components give rise to complex behavior is to investigate the rules by which cortical circuits are formed and acquire functionality during development. This review summarizes recent research on the development of the neocortex, from genetic determination in neural stem cells through to the dynamic role that specific neuronal populations play in the earliest circuits of neocortex, and how they contribute to emergent function and cognition. While many of these endeavors take advantage of model systems, consideration will also be given to advances in our understanding of activity in nascent human circuits. Such cross-species perspective is imperative when investigating the mechanisms underlying the dysfunction of early neocortical circuits in neurodevelopmental disorders, so that one can identify targets amenable to therapeutic intervention.","lang":"eng"}],"year":"2021","citation":{"ista":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, De Marco García NV, Cardin JA, Voytek B, Muotri AR. 2021. The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. 41(5), 813–822.","ieee":"I. L. Hanganu-Opatz <i>et al.</i>, “The logic of developing neocortical circuits in health and disease,” <i>The Journal of Neuroscience</i>, vol. 41, no. 5. Society for Neuroscience, pp. 813–822, 2021.","ama":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, et al. The logic of developing neocortical circuits in health and disease. <i>The Journal of Neuroscience</i>. 2021;41(5):813-822. doi:<a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">10.1523/jneurosci.1655-20.2020</a>","chicago":"Hanganu-Opatz, Ileana L., Simon J. B. Butt, Simon Hippenmeyer, Natalia V. De Marco García, Jessica A. Cardin, Bradley Voytek, and Alysson R. Muotri. “The Logic of Developing Neocortical Circuits in Health and Disease.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2021. <a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">https://doi.org/10.1523/jneurosci.1655-20.2020</a>.","short":"I.L. Hanganu-Opatz, S.J.B. Butt, S. Hippenmeyer, N.V. De Marco García, J.A. Cardin, B. Voytek, A.R. Muotri, The Journal of Neuroscience 41 (2021) 813–822.","apa":"Hanganu-Opatz, I. L., Butt, S. J. B., Hippenmeyer, S., De Marco García, N. V., Cardin, J. A., Voytek, B., &#38; Muotri, A. R. (2021). The logic of developing neocortical circuits in health and disease. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">https://doi.org/10.1523/jneurosci.1655-20.2020</a>","mla":"Hanganu-Opatz, Ileana L., et al. “The Logic of Developing Neocortical Circuits in Health and Disease.” <i>The Journal of Neuroscience</i>, vol. 41, no. 5, Society for Neuroscience, 2021, pp. 813–22, doi:<a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">10.1523/jneurosci.1655-20.2020</a>."},"oa":1,"volume":41,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Hanganu-Opatz, Ileana L.","last_name":"Hanganu-Opatz","first_name":"Ileana L."},{"full_name":"Butt, Simon J. B.","last_name":"Butt","first_name":"Simon J. B."},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"last_name":"De Marco García","first_name":"Natalia V.","full_name":"De Marco García, Natalia V."},{"last_name":"Cardin","first_name":"Jessica A.","full_name":"Cardin, Jessica A."},{"full_name":"Voytek, Bradley","first_name":"Bradley","last_name":"Voytek"},{"full_name":"Muotri, Alysson R.","first_name":"Alysson R.","last_name":"Muotri"}],"publication":"The Journal of Neuroscience","date_updated":"2023-09-05T14:03:17Z","ec_funded":1,"department":[{"_id":"SiHi"}],"intvolume":"        41"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cold Spring Harbor Laboratory","author":[{"full_name":"Anderson, Donovan J.","first_name":"Donovan J.","last_name":"Anderson"},{"last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"full_name":"McKenna, Aaron","last_name":"McKenna","first_name":"Aaron"},{"first_name":"Jay","last_name":"Shendure","full_name":"Shendure, Jay"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"},{"first_name":"Marshall S.","last_name":"Horwitz","full_name":"Horwitz, Marshall S."}],"oa":1,"date_published":"2021-01-01T00:00:00Z","type":"preprint","language":[{"iso":"eng"}],"status":"public","publication":"bioRxiv","ec_funded":1,"date_updated":"2021-02-04T07:29:53Z","month":"01","department":[{"_id":"SiHi"}],"day":"01","acknowledgement":"We thank Bill Bolosky, Microsoft Research, for earlier work showing proof of concept in TCGA\r\nbulk RNA-seq data. Supported by the Paul G. Allen Frontiers Group (University of Washington);\r\nNIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b] life science call grant\r\n(C13-002) to SH, and the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation program 725780 LinPro to SH.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.12.31.425016"}],"doi":"10.1101/2020.12.31.425016","article_processing_charge":"No","oa_version":"Preprint","title":"Simultaneous identification of brain cell type and lineage via single cell RNA sequencing","publication_status":"submitted","abstract":[{"lang":"eng","text":"Acquired mutations are sufficiently frequent such that the genome of a single cell offers a record of its history of cell divisions. Among more common somatic genomic alterations are loss of heterozygosity (LOH). Large LOH events are potentially detectable in single cell RNA sequencing (scRNA-seq) datasets as tracts of monoallelic expression for constitutionally heterozygous single nucleotide variants (SNVs) located among contiguous genes. We identified runs of monoallelic expression, consistent with LOH, uniquely distributed throughout the genome in single cell brain cortex transcriptomes of F1 hybrids involving different inbred mouse strains. We then phylogenetically reconstructed single cell lineages and simultaneously identified cell types by corresponding gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. Compared to engineered recording systems, LOH events accumulate throughout the genome and across the lifetime of an organism, affording tremendous capacity for encoding lineage information and increasing resolution for later cell divisions. This approach can conceivably be computationally incorporated into scRNA-seq analysis and may be useful for organisms where genetic engineering is prohibitive, such as humans."}],"year":"2021","citation":{"ama":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>","ieee":"D. J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, and M. S. Horwitz, “Simultaneous identification of brain cell type and lineage via single cell RNA sequencing,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. bioRxiv, <a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>.","chicago":"Anderson, Donovan J., Florian Pauler, Aaron McKenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>.","apa":"Anderson, D. J., Pauler, F., McKenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (n.d.). Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>","short":"D.J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, BioRxiv (n.d.).","mla":"Anderson, Donovan J., et al. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>."},"_id":"9082","project":[{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"date_created":"2021-02-04T07:23:23Z"},{"department":[{"_id":"MiLe"}],"date_updated":"2023-08-07T13:39:37Z","ec_funded":1,"publication":"SciPost Physics","arxiv":1,"intvolume":"        10","volume":10,"oa":1,"author":[{"full_name":"Marchukov, Oleksandr","first_name":"Oleksandr","last_name":"Marchukov"},{"last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"9fd614b7ab49999e7267874df2582f7e","creator":"dernst","file_id":"9105","content_type":"application/pdf","date_updated":"2021-02-09T07:06:22Z","relation":"main_file","date_created":"2021-02-09T07:06:22Z","file_size":666512,"file_name":"2021_SciPostPhysics_Marchukov.pdf","success":1,"access_level":"open_access"}],"date_created":"2021-02-04T12:39:24Z","_id":"9093","citation":{"ama":"Marchukov O, Volosniev A. Shape of a sound wave in a weakly-perturbed Bose gas. <i>SciPost Physics</i>. 2021;10(2). doi:<a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">10.21468/scipostphys.10.2.025</a>","ieee":"O. Marchukov and A. Volosniev, “Shape of a sound wave in a weakly-perturbed Bose gas,” <i>SciPost Physics</i>, vol. 10, no. 2. SciPost Foundation, 2021.","ista":"Marchukov O, Volosniev A. 2021. Shape of a sound wave in a weakly-perturbed Bose gas. SciPost Physics. 10(2), 025.","mla":"Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed Bose Gas.” <i>SciPost Physics</i>, vol. 10, no. 2, 025, SciPost Foundation, 2021, doi:<a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">10.21468/scipostphys.10.2.025</a>.","chicago":"Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed Bose Gas.” <i>SciPost Physics</i>. SciPost Foundation, 2021. <a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">https://doi.org/10.21468/scipostphys.10.2.025</a>.","apa":"Marchukov, O., &#38; Volosniev, A. (2021). Shape of a sound wave in a weakly-perturbed Bose gas. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">https://doi.org/10.21468/scipostphys.10.2.025</a>","short":"O. Marchukov, A. Volosniev, SciPost Physics 10 (2021)."},"article_number":"025","year":"2021","abstract":[{"lang":"eng","text":"We employ the Gross-Pitaevskii equation to study acoustic emission generated in a uniform Bose gas by a static impurity. The impurity excites a sound-wave packet, which propagates through the gas. We calculate the shape of this wave packet in the limit of long wave lengths, and argue that it is possible to extract properties of the impurity by observing this shape. We illustrate here this possibility for a Bose gas with a trapped impurity atom -- an example of a relevant experimental setup. Presented results are general for all one-dimensional systems described by the nonlinear Schrödinger equation and can also be used in nonatomic systems, e.g., to analyze light propagation in nonlinear optical media. Finally, we calculate the shape of the sound-wave packet for a three-dimensional Bose gas assuming a spherically symmetric perturbation."}],"title":"Shape of a sound wave in a weakly-perturbed Bose gas","publication_status":"published","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-02-09T07:06:22Z","doi":"10.21468/scipostphys.10.2.025","publication_identifier":{"issn":["2542-4653"]},"acknowledgement":"We acknowledge fruitful discussions with Dr. Simos Mistakidis regarding beyond mean-field\r\neffects in our system. We also thank Prof. Maxim Olshanii for valuable suggestions to improve\r\nthe manuscript.O.V.M acknowledges the support from the National Science Foundation\r\nthrough grants No. PHY-1402249, No. PHY-1607221, and No. PHY-1912542 and the\r\nBinational (US-Israel) Science Foundation through grant No. 2015616, as well as by the Israel\r\nScience Foundation (grant No. 1287/17) and from the German Aeronautics and Space Administration\r\n(DLR) through Grant No. 50WM1957. This work has also received funding from\r\nthe DFG Project No.413495248 [VO 2437/1-1] and European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411\r\n(A. G. V.)","article_type":"original","isi":1,"month":"02","status":"public","ddc":["530"],"language":[{"iso":"eng"}],"type":"journal_article","external_id":{"isi":["000646783100027"],"arxiv":["2004.08075"]},"date_published":"2021-02-03T00:00:00Z","publisher":"SciPost Foundation","issue":"2","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","quality_controlled":"1","day":"03"},{"oa":1,"volume":220,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","first_name":"Alexander F","last_name":"Leithner"},{"full_name":"Altenburger, LM","last_name":"Altenburger","first_name":"LM"},{"full_name":"Hauschild, R","first_name":"R","last_name":"Hauschild"},{"orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","full_name":"Assen, Frank P","first_name":"Frank P","last_name":"Assen"},{"full_name":"Rottner, K","last_name":"Rottner","first_name":"K"},{"last_name":"TEB","first_name":"Stradal","full_name":"TEB, Stradal"},{"full_name":"Diz-Muñoz, A","first_name":"A","last_name":"Diz-Muñoz"},{"full_name":"Stein, JV","last_name":"Stein","first_name":"JV"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"}],"publication":"Journal of Cell Biology","date_updated":"2023-09-05T13:57:53Z","department":[{"_id":"MiSi"}],"intvolume":"       220","file_date_updated":"2022-05-12T14:16:21Z","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","title":"Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse","article_type":"original","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"doi":"10.1083/jcb.202006081","scopus_import":"1","_id":"9094","file":[{"date_created":"2022-05-12T14:16:21Z","date_updated":"2022-05-12T14:16:21Z","file_size":5102328,"relation":"main_file","file_name":"2021_JournCellBiology_Leithner.pdf","access_level":"open_access","success":1,"checksum":"843ebc153847c8626e13c9c5ce71d533","creator":"dernst","file_id":"11367","content_type":"application/pdf"}],"date_created":"2021-02-05T10:08:04Z","abstract":[{"text":"Dendritic cells (DCs) are crucial for the priming of naive T cells and the initiation of adaptive immunity. Priming is initiated at a heterologous cell–cell contact, the immunological synapse (IS). While it is established that F-actin dynamics regulates signaling at the T cell side of the contact, little is known about the cytoskeletal contribution on the DC side. Here, we show that the DC actin cytoskeleton is decisive for the formation of a multifocal synaptic structure, which correlates with T cell priming efficiency. DC actin at the IS appears in transient foci that are dynamized by the WAVE regulatory complex (WRC). The absence of the WRC in DCs leads to stabilized contacts with T cells, caused by an increase in ICAM1-integrin–mediated cell–cell adhesion. This results in lower numbers of activated and proliferating T cells, demonstrating an important role for DC actin in the regulation of immune synapse functionality.","lang":"eng"}],"article_number":"e202006081","year":"2021","citation":{"short":"A.F. Leithner, L. Altenburger, R. Hauschild, F.P. Assen, K. Rottner, S. TEB, A. Diz-Muñoz, J. Stein, M.K. Sixt, Journal of Cell Biology 220 (2021).","apa":"Leithner, A. F., Altenburger, L., Hauschild, R., Assen, F. P., Rottner, K., TEB, S., … Sixt, M. K. (2021). Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202006081\">https://doi.org/10.1083/jcb.202006081</a>","chicago":"Leithner, Alexander F, LM Altenburger, R Hauschild, Frank P Assen, K Rottner, Stradal TEB, A Diz-Muñoz, JV Stein, and Michael K Sixt. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2021. <a href=\"https://doi.org/10.1083/jcb.202006081\">https://doi.org/10.1083/jcb.202006081</a>.","mla":"Leithner, Alexander F., et al. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” <i>Journal of Cell Biology</i>, vol. 220, no. 4, e202006081, Rockefeller University Press, 2021, doi:<a href=\"https://doi.org/10.1083/jcb.202006081\">10.1083/jcb.202006081</a>.","ama":"Leithner AF, Altenburger L, Hauschild R, et al. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. <i>Journal of Cell Biology</i>. 2021;220(4). doi:<a href=\"https://doi.org/10.1083/jcb.202006081\">10.1083/jcb.202006081</a>","ieee":"A. F. Leithner <i>et al.</i>, “Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse,” <i>Journal of Cell Biology</i>, vol. 220, no. 4. Rockefeller University Press, 2021.","ista":"Leithner AF, Altenburger L, Hauschild R, Assen FP, Rottner K, TEB S, Diz-Muñoz A, Stein J, Sixt MK. 2021. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. 220(4), e202006081."},"date_published":"2021-04-05T00:00:00Z","external_id":{"isi":["000626365700001"],"pmid":["33533935"]},"type":"journal_article","publisher":"Rockefeller University Press","pmid":1,"status":"public","month":"04","isi":1,"language":[{"iso":"eng"}],"ddc":["570"],"quality_controlled":"1","day":"05","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"has_accepted_license":"1","issue":"4"}]