[{"file_date_updated":"2020-12-06T17:30:09Z","doi":"10.1096/fj.201901543R","article_processing_charge":"No","pmid":1,"volume":33,"day":"01","publication":"FASEB Journal","date_published":"2019-12-01T00:00:00Z","intvolume":"        33","has_accepted_license":"1","page":"13734-13746","title":"Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses","oa":1,"quality_controlled":"1","date_created":"2019-12-15T23:00:42Z","citation":{"ista":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746.","ieee":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz, “Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses,” <i>FASEB Journal</i>, vol. 33, no. 12. FASEB, pp. 13734–13746, 2019.","short":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz, FASEB Journal 33 (2019) 13734–13746.","ama":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. <i>FASEB Journal</i>. 2019;33(12):13734-13746. doi:<a href=\"https://doi.org/10.1096/fj.201901543R\">10.1096/fj.201901543R</a>","chicago":"Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” <i>FASEB Journal</i>. FASEB, 2019. <a href=\"https://doi.org/10.1096/fj.201901543R\">https://doi.org/10.1096/fj.201901543R</a>.","apa":"Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., &#38; Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. <i>FASEB Journal</i>. FASEB. <a href=\"https://doi.org/10.1096/fj.201901543R\">https://doi.org/10.1096/fj.201901543R</a>","mla":"Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” <i>FASEB Journal</i>, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:<a href=\"https://doi.org/10.1096/fj.201901543R\">10.1096/fj.201901543R</a>."},"author":[{"first_name":"Lisa","full_name":"Klotz, Lisa","last_name":"Klotz"},{"full_name":"Wendler, Olaf","last_name":"Wendler","first_name":"Olaf"},{"first_name":"Renato","last_name":"Frischknecht","full_name":"Frischknecht, Renato"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"full_name":"Schulze, Holger","last_name":"Schulze","first_name":"Holger"},{"full_name":"Enz, Ralf","last_name":"Enz","first_name":"Ralf"}],"status":"public","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-06T14:34:36Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Glutamate is the major excitatory neurotransmitter in the CNS binding to a variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8) can act excitatory or inhibitory, depending on associated signal cascades. Expression and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3, and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants. Using receptor-specific antibodies in cochlear wholemounts, we found expression of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution and confocal microscopy in combination with 3-dimensional reconstructions indicated a postsynaptic localization of mGluR2 that overlaps with postsynaptic density protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast, mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary, we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament for new therapeutical strategies that could protect the cochlea against noxious stimuli and excitotoxicity."}],"month":"12","year":"2019","isi":1,"publication_identifier":{"eissn":["15306860"]},"article_type":"original","department":[{"_id":"RySh"}],"publisher":"FASEB","issue":"12","_id":"7179","external_id":{"isi":["000507466100054"],"pmid":["31585509"]},"publication_status":"published","oa_version":"Submitted Version","file":[{"date_updated":"2020-12-06T17:30:09Z","content_type":"application/pdf","access_level":"open_access","date_created":"2020-12-06T17:30:09Z","checksum":"79e3b72481dc32489911121cf3b7d8d0","success":1,"file_size":4766789,"file_name":"Klotz et al 2019 EMBO Reports.pdf","relation":"main_file","creator":"shigemot","file_id":"8922"}],"ddc":["571","599"],"type":"journal_article"},{"volume":10,"publication":"Nature Communications","day":"01","pmid":1,"has_accepted_license":"1","intvolume":"        10","date_published":"2019-12-01T00:00:00Z","doi":"10.1038/s41467-019-13543-1","file_date_updated":"2020-07-14T12:47:52Z","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","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"},"article_number":"5516","oa":1,"citation":{"chicago":"Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská, Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-13543-1\">https://doi.org/10.1038/s41467-019-13543-1</a>.","apa":"Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek, J., &#38; Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-13543-1\">https://doi.org/10.1038/s41467-019-13543-1</a>","mla":"Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” <i>Nature Communications</i>, vol. 10, 5516, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-13543-1\">10.1038/s41467-019-13543-1</a>.","ieee":"K. Retzer <i>et al.</i>, “Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","short":"K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek, C. Luschnig, Nature Communications 10 (2019).","ista":"Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J, Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516.","ama":"Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-13543-1\">10.1038/s41467-019-13543-1</a>"},"date_created":"2019-12-15T23:00:43Z","quality_controlled":"1","title":"Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter","date_updated":"2023-09-06T14:08:21Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation.","lang":"eng"}],"scopus_import":"1","author":[{"full_name":"Retzer, Katarzyna","last_name":"Retzer","first_name":"Katarzyna"},{"id":"3425EC26-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Akhmanova, Maria","last_name":"Akhmanova","orcid":"0000-0003-1522-3162"},{"full_name":"Konstantinova, Nataliia","last_name":"Konstantinova","first_name":"Nataliia"},{"first_name":"Kateřina","full_name":"Malínská, Kateřina","last_name":"Malínská"},{"last_name":"Leitner","full_name":"Leitner, Johannes","first_name":"Johannes"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"last_name":"Luschnig","full_name":"Luschnig, Christian","first_name":"Christian"}],"status":"public","publisher":"Springer Nature","type":"journal_article","file":[{"file_id":"7184","creator":"dernst","relation":"main_file","file_name":"2019_NatureComm_Retzer.pdf","checksum":"77e8720a8e0f3091b98159f85be40893","file_size":5156533,"date_created":"2019-12-16T07:37:50Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:52Z"}],"oa_version":"Published Version","ddc":["570"],"_id":"7180","publication_status":"published","external_id":{"isi":["000500508100001"],"pmid":["31797871"]},"isi":1,"publication_identifier":{"eissn":["20411723"]},"month":"12","year":"2019","project":[{"grant_number":"M02379","_id":"264CBBAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modeling epithelial tissue mechanics during cell invasion"}],"department":[{"_id":"DaSi"}],"article_type":"original"},{"type":"journal_article","oa_version":"Submitted Version","publication_status":"published","external_id":{"pmid":["31792410"],"isi":["000500748900021"]},"issue":"12","_id":"7181","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"article_type":"original","publication_identifier":{"issn":["10870156"],"eissn":["15461696"]},"isi":1,"project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales"}],"month":"12","year":"2019","related_material":{"record":[{"id":"13059","status":"public","relation":"research_data"}]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/","open_access":"1"}],"abstract":[{"lang":"eng","text":"Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6."}],"scopus_import":"1","date_updated":"2023-09-06T14:32:52Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"status":"public","author":[{"first_name":"Edgar","full_name":"Garriga, Edgar","last_name":"Garriga"},{"first_name":"Paolo","last_name":"Di Tommaso","full_name":"Di Tommaso, Paolo"},{"first_name":"Cedrik","last_name":"Magis","full_name":"Magis, Cedrik"},{"first_name":"Ionas","full_name":"Erb, Ionas","last_name":"Erb"},{"last_name":"Mansouri","full_name":"Mansouri, Leila","first_name":"Leila"},{"first_name":"Athanasios","full_name":"Baltzis, Athanasios","last_name":"Baltzis"},{"full_name":"Laayouni, Hafid","last_name":"Laayouni","first_name":"Hafid"},{"full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Evan","last_name":"Floden","full_name":"Floden, Evan"},{"first_name":"Cedric","full_name":"Notredame, Cedric","last_name":"Notredame"}],"citation":{"ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. <i>Nature Biotechnology</i>. 2019;37(12):1466-1470. doi:<a href=\"https://doi.org/10.1038/s41587-019-0333-6\">10.1038/s41587-019-0333-6</a>","ieee":"E. Garriga <i>et al.</i>, “Large multiple sequence alignments with a root-to-leaf regressive method,” <i>Nature Biotechnology</i>, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.","short":"E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.","ista":"Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.","apa":"Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-019-0333-6\">https://doi.org/10.1038/s41587-019-0333-6</a>","chicago":"Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” <i>Nature Biotechnology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41587-019-0333-6\">https://doi.org/10.1038/s41587-019-0333-6</a>.","mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” <i>Nature Biotechnology</i>, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:<a href=\"https://doi.org/10.1038/s41587-019-0333-6\">10.1038/s41587-019-0333-6</a>."},"date_created":"2019-12-15T23:00:43Z","quality_controlled":"1","oa":1,"title":"Large multiple sequence alignments with a root-to-leaf regressive method","page":"1466-1470","intvolume":"        37","date_published":"2019-12-01T00:00:00Z","publication":"Nature Biotechnology","day":"01","volume":37,"pmid":1,"ec_funded":1,"article_processing_charge":"No","doi":"10.1038/s41587-019-0333-6"},{"doi":"10.3389/fpls.2019.01437","file_date_updated":"2020-07-14T12:47:52Z","tmp":{"short":"CC BY (4.0)","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"},"article_processing_charge":"No","publication":"Frontiers in Plant Science","day":"14","volume":10,"pmid":1,"intvolume":"        10","has_accepted_license":"1","date_published":"2019-11-14T00:00:00Z","title":"Systematic Y2H screening reveals extensive effector-complex formation","oa":1,"article_number":"1437","citation":{"apa":"Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S., … Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex formation. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2019.01437\">https://doi.org/10.3389/fpls.2019.01437</a>","chicago":"Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” <i>Frontiers in Plant Science</i>. Frontiers, 2019. <a href=\"https://doi.org/10.3389/fpls.2019.01437\">https://doi.org/10.3389/fpls.2019.01437</a>.","mla":"Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” <i>Frontiers in Plant Science</i>, vol. 10, no. 11, 1437, Frontiers, 2019, doi:<a href=\"https://doi.org/10.3389/fpls.2019.01437\">10.3389/fpls.2019.01437</a>.","ama":"Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. <i>Frontiers in Plant Science</i>. 2019;10(11). doi:<a href=\"https://doi.org/10.3389/fpls.2019.01437\">10.3389/fpls.2019.01437</a>","ieee":"A. Alcântara <i>et al.</i>, “Systematic Y2H screening reveals extensive effector-complex formation,” <i>Frontiers in Plant Science</i>, vol. 10, no. 11. Frontiers, 2019.","ista":"Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.","short":"A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A. Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science 10 (2019)."},"date_created":"2019-12-15T23:00:43Z","quality_controlled":"1","status":"public","author":[{"last_name":"Alcântara","full_name":"Alcântara, André","first_name":"André"},{"first_name":"Jason","full_name":"Bosch, Jason","last_name":"Bosch"},{"first_name":"Fahimeh","full_name":"Nazari, Fahimeh","last_name":"Nazari"},{"first_name":"Gesa","full_name":"Hoffmann, Gesa","last_name":"Hoffmann"},{"orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Uhse, Simon","last_name":"Uhse","first_name":"Simon"},{"full_name":"Darino, Martin A.","last_name":"Darino","first_name":"Martin A."},{"first_name":"Toluwase","last_name":"Olukayode","full_name":"Olukayode, Toluwase"},{"full_name":"Reumann, Daniel","last_name":"Reumann","first_name":"Daniel"},{"last_name":"Baggaley","full_name":"Baggaley, Laura","first_name":"Laura"},{"first_name":"Armin","last_name":"Djamei","full_name":"Djamei, Armin"}],"date_updated":"2023-09-06T14:33:46Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["1664462X"]},"isi":1,"year":"2019","month":"11","department":[{"_id":"JiFr"}],"article_type":"original","publisher":"Frontiers","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:52Z","file_size":1532505,"checksum":"995aa838aec2064d93550de82b40bbd1","date_created":"2019-12-16T07:58:43Z","file_name":"2019_FrontiersPlant_Alcantara.pdf","creator":"dernst","file_id":"7185","relation":"main_file"}],"ddc":["580"],"oa_version":"Published Version","type":"journal_article","publication_status":"published","external_id":{"isi":["000499821700001"],"pmid":["31803201"]},"issue":"11","_id":"7182"},{"alternative_title":["LNCS"],"external_id":{"arxiv":["1907.11010"],"isi":["000723515700027"]},"publication_status":"published","_id":"7183","type":"conference","oa_version":"Preprint","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"year":"2019","month":"10","publication_identifier":{"eissn":["16113349"],"isbn":["9783030317836"],"issn":["03029743"]},"isi":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.11010"}],"abstract":[{"lang":"eng","text":"A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2)."}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-06T12:40:58Z","status":"public","author":[{"first_name":"Tomás","full_name":"Brázdil, Tomás","last_name":"Brázdil"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Antonín","full_name":"Kucera, Antonín","last_name":"Kucera"},{"last_name":"Novotný","full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"first_name":"Dominik","full_name":"Velan, Dominik","last_name":"Velan"}],"quality_controlled":"1","arxiv":1,"conference":{"end_date":"2019-10-31","location":"Taipei, Taiwan","start_date":"2019-10-28","name":"ATVA: Automated TEchnology for Verification and Analysis"},"date_created":"2019-12-15T23:00:44Z","citation":{"short":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2019, pp. 462–478.","ista":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast termination for probabilistic VASS with nondeterminism. International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology for Verification and Analysis, LNCS, vol. 11781, 462–478.","ieee":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in <i>International Symposium on Automated Technology for Verification and Analysis</i>, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478.","ama":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: <i>International Symposium on Automated Technology for Verification and Analysis</i>. Vol 11781. Springer Nature; 2019:462-478. doi:<a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">10.1007/978-3-030-31784-3_27</a>","mla":"Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” <i>International Symposium on Automated Technology for Verification and Analysis</i>, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:<a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">10.1007/978-3-030-31784-3_27</a>.","chicago":"Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In <i>International Symposium on Automated Technology for Verification and Analysis</i>, 11781:462–78. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">https://doi.org/10.1007/978-3-030-31784-3_27</a>.","apa":"Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., &#38; Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In <i>International Symposium on Automated Technology for Verification and Analysis</i> (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">https://doi.org/10.1007/978-3-030-31784-3_27</a>"},"oa":1,"title":"Deciding fast termination for probabilistic VASS with nondeterminism","page":"462-478","date_published":"2019-10-21T00:00:00Z","intvolume":"     11781","publication":"International Symposium on Automated Technology for Verification and Analysis","day":"21","volume":11781,"article_processing_charge":"No","doi":"10.1007/978-3-030-31784-3_27"},{"_id":"7186","alternative_title":["ISTA Thesis"],"publication_status":"published","type":"dissertation","oa_version":"Published Version","file":[{"checksum":"585583c1c875c5d9525703a539668a7c","file_size":19431292,"date_created":"2019-12-19T15:18:11Z","content_type":"application/zip","access_level":"closed","date_updated":"2020-07-14T12:47:52Z","creator":"cschwayer","file_id":"7194","relation":"source_file","file_name":"DocumentSourceFiles.zip"},{"file_name":"Thesis_CS_final.pdf","creator":"cschwayer","file_id":"7195","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:52Z","file_size":19226428,"checksum":"9b9b24351514948d27cec659e632e2cd","date_created":"2019-12-19T15:19:21Z"}],"ddc":["570"],"supervisor":[{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaHe"}],"year":"2019","month":"12","publication_identifier":{"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"Tissue morphogenesis in developmental or physiological processes is regulated by molecular\r\nand mechanical signals. While the molecular signaling cascades are increasingly well\r\ndescribed, the mechanical signals affecting tissue shape changes have only recently been\r\nstudied in greater detail. To gain more insight into the mechanochemical and biophysical\r\nbasis of an epithelial spreading process (epiboly) in early zebrafish development, we studied\r\ncell-cell junction formation and actomyosin network dynamics at the boundary between\r\nsurface layer epithelial cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,\r\nthe cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the end of\r\ngastrulation. It has been previously shown that an actomyosin ring residing within the YSL\r\npulls on the EVL tissue through a cable-constriction and a flow-friction motor, thereby\r\ndragging the tissue vegetal wards. Pulling forces are likely transmitted from the YSL\r\nactomyosin ring to EVL cells; however, the nature and formation of the junctional structure\r\nmediating this process has not been well described so far. Therefore, our main aim was to\r\ndetermine the nature, dynamics and potential function of the EVL-YSL junction during this\r\nepithelial tissue spreading. Specifically, we show that the EVL-YSL junction is a\r\nmechanosensitive structure, predominantly made of tight junction (TJ) proteins. The process\r\nof TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated\r\nZonula Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly, we\r\ncould demonstrate that ZO-1 is present in a non-junctional pool on the surface of the yolk\r\ncell, and ZO-1 undergoes a phase separation process that likely renders the protein\r\nresponsive to flows. These flows are directed towards the junction and mediate proper\r\ntension-dependent recruitment of ZO-1. Upon reaching the EVL-YSL junction ZO-1 gets\r\nincorporated into the junctional pool mediated through its direct actin-binding domain.\r\nWhen the non-junctional pool and/or ZO-1 direct actin binding is absent, TJs fail in their\r\nproper mechanosensitive responses resulting in slower tissue spreading. We could further\r\ndemonstrate that depletion of ZO proteins within the YSL results in diminished actomyosin\r\nring formation. This suggests that a mechanochemical feedback loop is at work during\r\nzebrafish epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin\r\ncontractility and flows positively influence ZO-1 junctional recruitment. Finally, such a\r\nmesoscale polarization process mediated through the flow of phase-separated protein\r\nclusters might have implications for other processes such as immunological synapse\r\nformation, C. elegans zygote polarization and wound healing."}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1096"},{"id":"7001","relation":"part_of_dissertation","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-07T12:56:42Z","author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","full_name":"Schwayer, Cornelia","last_name":"Schwayer","orcid":"0000-0001-5130-2226"}],"status":"public","citation":{"short":"C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow, Institute of Science and Technology Austria, 2019.","ista":"Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria.","ieee":"C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Institute of Science and Technology Austria, 2019.","ama":"Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7186\">10.15479/AT:ISTA:7186</a>","mla":"Schwayer, Cornelia. <i>Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7186\">10.15479/AT:ISTA:7186</a>.","chicago":"Schwayer, Cornelia. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7186\">https://doi.org/10.15479/AT:ISTA:7186</a>.","apa":"Schwayer, C. (2019). <i>Mechanosensation of tight junctions depends on ZO-1 phase separation and flow</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7186\">https://doi.org/10.15479/AT:ISTA:7186</a>"},"date_created":"2019-12-16T14:26:14Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"SSU"}],"oa":1,"title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","page":"107","date_published":"2019-12-16T00:00:00Z","has_accepted_license":"1","degree_awarded":"PhD","day":"16","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:52Z","doi":"10.15479/AT:ISTA:7186"},{"department":[{"_id":"MiLe"}],"article_type":"original","publication_identifier":{"issn":["2643-1564"]},"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"year":"2019","month":"12","oa_version":"Published Version","type":"journal_article","ddc":["530"],"file":[{"date_created":"2019-12-18T07:13:14Z","file_size":1370022,"checksum":"382eb67e62a77052a23887332d363f96","date_updated":"2020-07-14T12:47:52Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"7193","creator":"dernst","file_name":"2019_PhysRevResearch_Huber.pdf"}],"external_id":{"arxiv":["1908.02483"]},"publication_status":"published","issue":"3","_id":"7190","publisher":"American Physical Society","status":"public","author":[{"last_name":"Huber","full_name":"Huber, D.","first_name":"D."},{"last_name":"Hammer","full_name":"Hammer, H.-W.","first_name":"H.-W."},{"full_name":"Volosniev, Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem"}],"abstract":[{"lang":"eng","text":"We investigate the ground-state energy of a one-dimensional Fermi gas with two bosonic impurities. We consider spinless fermions with no fermion-fermion interactions. The fermion-impurity and impurity-impurity interactions are modeled with Dirac delta functions. First, we study the case where impurity and fermion have equal masses, and the impurity-impurity two-body interaction is identical to the fermion-impurity interaction, such that the system is solvable with the Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity subsystem is below the energy of the bound state that exists without the Fermi gas. We interpret this as a manifestation of attractive boson-boson interactions induced by the fermionic medium, and refer to the impurity-impurity subsystem as an in-medium bound state. For repulsive interactions, we find no in-medium bound states. Second, we construct an effective model to describe these interactions, and compare its predictions to the exact solution. We use this effective model to study nonintegrable systems with unequal masses and/or potentials. We discuss parameter regimes for which impurity-impurity attraction induced by the Fermi gas can lead to the formation of in-medium bound states made of bosons that repel each other in the absence of the Fermi gas."}],"date_updated":"2024-02-28T13:11:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"title":"In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas","citation":{"ieee":"D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas,” <i>Physical Review Research</i>, vol. 1, no. 3. American Physical Society, 2019.","short":"D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).","ista":"Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177.","ama":"Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. <i>Physical Review Research</i>. 2019;1(3). doi:<a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">10.1103/physrevresearch.1.033177</a>","mla":"Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” <i>Physical Review Research</i>, vol. 1, no. 3, 033177, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">10.1103/physrevresearch.1.033177</a>.","chicago":"Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” <i>Physical Review Research</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">https://doi.org/10.1103/physrevresearch.1.033177</a>.","apa":"Huber, D., Hammer, H.-W., &#38; Volosniev, A. (2019). In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">https://doi.org/10.1103/physrevresearch.1.033177</a>"},"date_created":"2019-12-17T13:03:41Z","quality_controlled":"1","arxiv":1,"oa":1,"article_number":"033177","tmp":{"short":"CC BY (4.0)","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"},"article_processing_charge":"No","ec_funded":1,"doi":"10.1103/physrevresearch.1.033177","file_date_updated":"2020-07-14T12:47:52Z","intvolume":"         1","has_accepted_license":"1","date_published":"2019-12-16T00:00:00Z","publication":"Physical Review Research","day":"16","volume":1},{"title":"Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA","quality_controlled":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"citation":{"mla":"Dos Santos Caldas, Paulo R., et al. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” <i>Nature Communications</i>, vol. 10, 5744, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-13702-4\">10.1038/s41467-019-13702-4</a>.","apa":"Dos Santos Caldas, P. R., Lopez Pelegrin, M. D., Pearce, D. J. G., Budanur, N. B., Brugués, J., &#38; Loose, M. (2019). Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-13702-4\">https://doi.org/10.1038/s41467-019-13702-4</a>","chicago":"Dos Santos Caldas, Paulo R, Maria D Lopez Pelegrin, Daniel J. G. Pearce, Nazmi B Budanur, Jan Brugués, and Martin Loose. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-13702-4\">https://doi.org/10.1038/s41467-019-13702-4</a>.","ama":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-13702-4\">10.1038/s41467-019-13702-4</a>","ieee":"P. R. Dos Santos Caldas, M. D. Lopez Pelegrin, D. J. G. Pearce, N. B. Budanur, J. Brugués, and M. Loose, “Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","short":"P.R. Dos Santos Caldas, M.D. Lopez Pelegrin, D.J.G. Pearce, N.B. Budanur, J. Brugués, M. Loose, Nature Communications 10 (2019).","ista":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. 2019. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 10, 5744."},"date_created":"2019-12-20T12:22:57Z","oa":1,"article_number":"5744","tmp":{"short":"CC BY (4.0)","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"},"article_processing_charge":"No","ec_funded":1,"file_date_updated":"2020-07-14T12:47:53Z","doi":"10.1038/s41467-019-13702-4","date_published":"2019-12-17T00:00:00Z","has_accepted_license":"1","intvolume":"        10","publication":"Nature Communications","day":"17","volume":10,"article_type":"original","department":[{"_id":"MaLo"},{"_id":"BjHo"}],"project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"month":"12","year":"2019","publication_identifier":{"issn":["2041-1723"]},"isi":1,"publication_status":"published","external_id":{"isi":["000503009300001"]},"_id":"7197","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:53Z","checksum":"a1b44b427ba341383197790d0e8789fa","file_size":8488733,"date_created":"2019-12-23T07:34:56Z","file_name":"2019_NatureComm_Caldas.pdf","file_id":"7208","creator":"dernst","relation":"main_file"}],"type":"journal_article","oa_version":"Published Version","ddc":["570"],"publisher":"Springer Nature","status":"public","author":[{"first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","full_name":"Dos Santos Caldas, Paulo R","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461"},{"first_name":"Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Pelegrin","full_name":"Lopez Pelegrin, Maria D"},{"last_name":"Pearce","full_name":"Pearce, Daniel J. G.","first_name":"Daniel J. G."},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"},{"full_name":"Brugués, Jan","last_name":"Brugués","first_name":"Jan"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"scopus_import":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8358"}]},"abstract":[{"text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-07T13:18:51Z"},{"day":"25","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","volume":55,"intvolume":"        55","date_published":"2019-09-25T00:00:00Z","doi":"10.1214/18-AIHP916","ec_funded":1,"article_processing_charge":"No","oa":1,"date_created":"2018-12-11T11:44:29Z","citation":{"ama":"Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP with non-random initial condition. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. 2019;55(3):1203-1225. doi:<a href=\"https://doi.org/10.1214/18-AIHP916\">10.1214/18-AIHP916</a>","short":"P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 1203–1225.","ista":"Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 55(3), 1203–1225.","ieee":"P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle in TASEP with non-random initial condition,” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 55, no. 3. Institute of Mathematical Statistics, pp. 1203–1225, 2019.","mla":"Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 55, no. 3, Institute of Mathematical Statistics, 2019, pp. 1203–25, doi:<a href=\"https://doi.org/10.1214/18-AIHP916\">10.1214/18-AIHP916</a>.","apa":"Ferrari, P., Ghosal, P., &#38; Nejjar, P. (2019). Limit law of a second class particle in TASEP with non-random initial condition. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-AIHP916\">https://doi.org/10.1214/18-AIHP916</a>","chicago":"Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics, 2019. <a href=\"https://doi.org/10.1214/18-AIHP916\">https://doi.org/10.1214/18-AIHP916</a>."},"arxiv":1,"quality_controlled":"1","page":"1203-1225","title":"Limit law of a second class particle in TASEP with non-random initial condition","date_updated":"2023-10-17T08:53:45Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/1710.02323","open_access":"1"}],"abstract":[{"text":"We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ&lt;λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t.","lang":"eng"}],"scopus_import":"1","status":"public","author":[{"full_name":"Ferrari, Patrick","last_name":"Ferrari","first_name":"Patrick"},{"full_name":"Ghosal, Promit","last_name":"Ghosal","first_name":"Promit"},{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Nejjar","full_name":"Nejjar, Peter"}],"publisher":"Institute of Mathematical Statistics","oa_version":"Preprint","type":"journal_article","publication_status":"published","external_id":{"isi":["000487763200001"],"arxiv":["1710.02323"]},"issue":"3","_id":"72","publication_identifier":{"issn":["0246-0203"]},"isi":1,"project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"}],"month":"09","year":"2019","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"article_type":"original"},{"status":"public","author":[{"first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","last_name":"Brighi"},{"full_name":"Grilli, Marco","last_name":"Grilli","first_name":"Marco"},{"last_name":"Leridon","full_name":"Leridon, Brigitte","first_name":"Brigitte"},{"full_name":"Caprara, Sergio","last_name":"Caprara","first_name":"Sergio"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1907.13579","open_access":"1"}],"abstract":[{"text":"Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting films found an emergent inhomogeneity at the scale of tens of nanometers. This inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity measured in transport above the superconducting critical temperature Tc. This behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper pairs that display a quasiconfinement (i.e., a slowing down of their diffusive dynamics) on length scales shorter than the inhomogeneity identified by tunneling experiments. Here, we assume this anomalous diffusive behavior of fluctuating Cooper pairs and calculate the effect of these fluctuations on the electron density of states above Tc. We find that the density of states is substantially suppressed up to temperatures well above Tc. This behavior, which is closely reminiscent of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper pairs in the absence of stable preformed pairs, setting the stage for an intermediate behavior between the two common paradigms in the superconducting-insulator transition, namely, the localization of Cooper pairs (the so-called bosonic scenario) and the breaking of Cooper pairs into unpaired electrons due to strong disorder (the so-called fermionic scenario).","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2024-02-28T13:14:08Z","article_type":"original","department":[{"_id":"MaSe"}],"month":"11","year":"2019","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"isi":1,"external_id":{"arxiv":["1907.13579"],"isi":["000498845700006"]},"publication_status":"published","_id":"7200","issue":"17","type":"journal_article","oa_version":"Preprint","publisher":"American Physical Society","article_processing_charge":"No","doi":"10.1103/PhysRevB.100.174518","date_published":"2019-11-25T00:00:00Z","intvolume":"       100","day":"25","publication":"Physical Review B","volume":100,"title":"Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films","quality_controlled":"1","arxiv":1,"citation":{"mla":"Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” <i>Physical Review B</i>, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">10.1103/PhysRevB.100.174518</a>.","apa":"Brighi, P., Grilli, M., Leridon, B., &#38; Caprara, S. (2019). Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">https://doi.org/10.1103/PhysRevB.100.174518</a>","chicago":"Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">https://doi.org/10.1103/PhysRevB.100.174518</a>.","ama":"Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. <i>Physical Review B</i>. 2019;100(17). doi:<a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">10.1103/PhysRevB.100.174518</a>","ista":"Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 100(17), 174518.","short":"P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).","ieee":"P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films,” <i>Physical Review B</i>, vol. 100, no. 17. American Physical Society, 2019."},"date_created":"2019-12-22T23:00:41Z","oa":1,"article_number":"174518"},{"date_published":"2019-11-17T00:00:00Z","day":"17","publication":"International Conference for High Performance Computing, Networking, Storage and Analysis, SC","article_processing_charge":"No","ec_funded":1,"doi":"10.1145/3295500.3356222","date_created":"2019-12-22T23:00:42Z","citation":{"chicago":"Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3295500.3356222\">https://doi.org/10.1145/3295500.3356222</a>.","apa":"Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., &#38; Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>. Denver, CO, Unites States: ACM. <a href=\"https://doi.org/10.1145/3295500.3356222\">https://doi.org/10.1145/3295500.3356222</a>","mla":"Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>, a11, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3295500.3356222\">10.1145/3295500.3356222</a>.","ista":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML: High-performance sparse communication for machine learning. International Conference for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference for High Performance Computing, Networking, Storage and Analysis, a11.","short":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:, International Conference for High Performance Computing, Networking, Storage and Analysis, SC, ACM, 2019.","ieee":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>, Denver, CO, Unites States, 2019.","ama":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance sparse communication for machine learning. In: <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>. ACM; 2019. doi:<a href=\"https://doi.org/10.1145/3295500.3356222\">10.1145/3295500.3356222</a>"},"quality_controlled":"1","arxiv":1,"conference":{"end_date":"2019-11-19","location":"Denver, CO, Unites States","name":"SC: Conference for High Performance Computing, Networking, Storage and Analysis","start_date":"2019-11-17"},"oa":1,"article_number":"a11","title":"SparCML: High-performance sparse communication for machine learning","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.08021"}],"abstract":[{"text":"Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed \"data parallel\" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-09-06T14:37:55Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","author":[{"first_name":"Cedric","full_name":"Renggli, Cedric","last_name":"Renggli"},{"full_name":"Ashkboos, Saleh","last_name":"Ashkboos","id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A","first_name":"Saleh"},{"first_name":"Mehdi","last_name":"Aghagolzadeh","full_name":"Aghagolzadeh, Mehdi"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"last_name":"Hoefler","full_name":"Hoefler, Torsten","first_name":"Torsten"}],"type":"conference","oa_version":"Preprint","external_id":{"arxiv":["1802.08021"],"isi":["000545976800011"]},"publication_status":"published","_id":"7201","publisher":"ACM","department":[{"_id":"DaAl"}],"publication_identifier":{"issn":["21674329"],"isbn":["9781450362290"],"eissn":["21674337"]},"isi":1,"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223"}],"month":"11","year":"2019"},{"isi":1,"publication_identifier":{"eissn":["2050084X"]},"year":"2019","month":"11","project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416"}],"department":[{"_id":"SiHi"}],"article_type":"original","publisher":"eLife Sciences Publications","file":[{"file_name":"2019_eLife_Llorca.pdf","relation":"main_file","file_id":"7503","creator":"dernst","date_updated":"2020-07-14T12:47:53Z","access_level":"open_access","content_type":"application/pdf","date_created":"2020-02-18T15:19:26Z","file_size":2960543,"checksum":"b460ecc33e1a68265e7adea775021f3a"}],"type":"journal_article","oa_version":"Published Version","ddc":["570"],"_id":"7202","publication_status":"published","external_id":{"pmid":["31736464"],"isi":["000508156800001"]},"author":[{"last_name":"Llorca","full_name":"Llorca, Alfredo","first_name":"Alfredo"},{"full_name":"Ciceri, Gabriele","last_name":"Ciceri","first_name":"Gabriele"},{"first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","last_name":"Beattie","full_name":"Beattie, Robert J"},{"first_name":"Fong Kuan","last_name":"Wong","full_name":"Wong, Fong Kuan"},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"first_name":"Eleni","full_name":"Serafeimidou-Pouliou, Eleni","last_name":"Serafeimidou-Pouliou"},{"first_name":"Marian","last_name":"Fernández-Otero","full_name":"Fernández-Otero, Marian"},{"full_name":"Streicher, Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"last_name":"Arnold","full_name":"Arnold, Sebastian J.","first_name":"Sebastian J."},{"first_name":"Martin","full_name":"Meyer, Martin","last_name":"Meyer"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"last_name":"Maravall","full_name":"Maravall, Miguel","first_name":"Miguel"},{"first_name":"Oscar","last_name":"Marín","full_name":"Marín, Oscar"}],"status":"public","date_updated":"2023-09-06T14:38:39Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas."}],"scopus_import":"1","title":"A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture","article_number":"e51381","oa":1,"citation":{"ama":"Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.51381\">10.7554/eLife.51381</a>","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, ELife 8 (2019).","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 8, e51381.","ieee":"A. Llorca <i>et al.</i>, “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou, E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.51381\">https://doi.org/10.7554/eLife.51381</a>","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.51381\">https://doi.org/10.7554/eLife.51381</a>.","mla":"Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” <i>ELife</i>, vol. 8, e51381, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.51381\">10.7554/eLife.51381</a>."},"date_created":"2019-12-22T23:00:42Z","quality_controlled":"1","doi":"10.7554/eLife.51381","file_date_updated":"2020-07-14T12:47:53Z","article_processing_charge":"No","ec_funded":1,"tmp":{"short":"CC BY (4.0)","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"},"volume":8,"publication":"eLife","day":"18","pmid":1,"has_accepted_license":"1","intvolume":"         8","date_published":"2019-11-18T00:00:00Z"},{"author":[{"last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"status":"public","abstract":[{"text":"The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants. But these amplifiers of natural selection typically increase fixation time. Here we study population structures that achieve a tradeoff between fixation probability and time. First, we show that no amplifiers can have an asymptotically lower absorption time than the well-mixed population. Then we design population structures that substantially augment the fixation probability with just a minor increase in fixation time. Finally, we show that those structures enable higher effective rate of evolution than the well-mixed population provided that the rate of generating advantageous mutants is relatively low. Our work sheds light on how population structure affects the rate of evolution. Moreover, our structures could be useful for lab-based, medical, or industrial applications of evolutionary optimization.","lang":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7196"}]},"scopus_import":"1","date_updated":"2023-09-07T13:19:22Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrCh"}],"article_type":"original","isi":1,"publication_identifier":{"issn":["2399-3642"]},"year":"2019","month":"04","project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"oa_version":"Published Version","type":"journal_article","ddc":["000"],"file":[{"file_name":"2019_CommBio_Tkadlec.pdf","relation":"main_file","creator":"dernst","file_id":"7211","date_updated":"2020-07-14T12:47:53Z","content_type":"application/pdf","access_level":"open_access","date_created":"2019-12-23T13:39:30Z","file_size":1670274,"checksum":"d1a69bfe73767e4246f0a38e4e1554dd"}],"_id":"7210","publication_status":"published","external_id":{"isi":["000465425700006"],"pmid":["31044163"]},"publisher":"Springer Nature","ec_funded":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","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"},"doi":"10.1038/s42003-019-0373-y","file_date_updated":"2020-07-14T12:47:53Z","intvolume":"         2","has_accepted_license":"1","date_published":"2019-04-23T00:00:00Z","volume":2,"publication":"Communications Biology","day":"23","pmid":1,"title":"Population structure determines the tradeoff between fixation probability and fixation time","citation":{"apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., &#38; Nowak, M. A. (2019). Population structure determines the tradeoff between fixation probability and fixation time. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-019-0373-y\">https://doi.org/10.1038/s42003-019-0373-y</a>","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” <i>Communications Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s42003-019-0373-y\">https://doi.org/10.1038/s42003-019-0373-y</a>.","mla":"Tkadlec, Josef, et al. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” <i>Communications Biology</i>, vol. 2, 138, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s42003-019-0373-y\">10.1038/s42003-019-0373-y</a>.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Population structure determines the tradeoff between fixation probability and fixation time. <i>Communications Biology</i>. 2019;2. doi:<a href=\"https://doi.org/10.1038/s42003-019-0373-y\">10.1038/s42003-019-0373-y</a>","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Communications Biology 2 (2019).","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Population structure determines the tradeoff between fixation probability and fixation time,” <i>Communications Biology</i>, vol. 2. Springer Nature, 2019.","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2019. Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. 2, 138."},"date_created":"2019-12-23T13:36:50Z","quality_controlled":"1","article_number":"138","oa":1},{"has_accepted_license":"1","intvolume":"        20","date_published":"2019-12-17T00:00:00Z","volume":20,"day":"17","publication":"BMC Bioinformatics","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","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"},"doi":"10.1186/s12859-019-3208-4","file_date_updated":"2020-07-14T12:47:54Z","date_created":"2019-12-29T23:00:46Z","citation":{"apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., &#38; Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. <i>BMC Bioinformatics</i>. BMC. <a href=\"https://doi.org/10.1186/s12859-019-3208-4\">https://doi.org/10.1186/s12859-019-3208-4</a>","chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” <i>BMC Bioinformatics</i>. BMC, 2019. <a href=\"https://doi.org/10.1186/s12859-019-3208-4\">https://doi.org/10.1186/s12859-019-3208-4</a>.","mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” <i>BMC Bioinformatics</i>, vol. 20, 641, BMC, 2019, doi:<a href=\"https://doi.org/10.1186/s12859-019-3208-4\">10.1186/s12859-019-3208-4</a>.","ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. <i>BMC Bioinformatics</i>. 2019;20. doi:<a href=\"https://doi.org/10.1186/s12859-019-3208-4\">10.1186/s12859-019-3208-4</a>","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” <i>BMC Bioinformatics</i>, vol. 20. BMC, 2019.","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641."},"quality_controlled":"1","article_number":"641","oa":1,"title":"Recovering rearranged cancer chromosomes from karyotype graphs","abstract":[{"text":"Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-09-06T14:51:06Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"author":[{"full_name":"Aganezov, Sergey","last_name":"Aganezov","first_name":"Sergey"},{"first_name":"Ilya","full_name":"Zban, Ilya","last_name":"Zban"},{"id":"2980135A-F248-11E8-B48F-1D18A9856A87","first_name":"Vitalii","last_name":"Aksenov","full_name":"Aksenov, Vitalii"},{"first_name":"Nikita","full_name":"Alexeev, Nikita","last_name":"Alexeev"},{"last_name":"Schatz","full_name":"Schatz, Michael C.","first_name":"Michael C."}],"status":"public","type":"journal_article","file":[{"date_created":"2020-01-02T16:10:58Z","file_size":1917374,"checksum":"7a30357efdcf8f66587ed495c0927724","date_updated":"2020-07-14T12:47:54Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"7221","file_name":"2019_BMCBioinfo_Aganezov.pdf"}],"ddc":["570"],"oa_version":"Published Version","_id":"7214","publication_status":"published","external_id":{"isi":["000511618800007"]},"publisher":"BMC","department":[{"_id":"DaAl"}],"article_type":"original","isi":1,"publication_identifier":{"eissn":["14712105"]},"month":"12","year":"2019"},{"publication":"2019 IEEE Intelligent Transportation Systems Conference","day":"28","date_updated":"2023-09-06T14:50:28Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We present LiveTraVeL (Live Transit Vehicle Labeling), a real-time system to label a stream of noisy observations of transit vehicle trajectories with the transit routes they are serving (e.g., northbound bus #5). In order to scale efficiently to large transit networks, our system first retrieves a small set of candidate routes from a geometrically indexed data structure, then applies a fine-grained scoring step to choose the best match. Given that real-time data remains unavailable for the majority of the world’s transit agencies, these inferences can help feed a real-time map of a transit system’s trips, infer transit trip delays in real time, or measure and correct noisy transit tracking data. This system can run on vehicle observations from a variety of sources that don’t attach route information to vehicle observations, such as public imagery streams or user-contributed transit vehicle sightings.We abstract away the specifics of the sensing system and demonstrate the effectiveness of our system on a \"semisynthetic\" dataset of all New York City buses, where we simulate sensed trajectories by starting with fully labeled vehicle trajectories reported via the GTFS-Realtime protocol, removing the transit route IDs, and perturbing locations with synthetic noise. Using just the geometric shapes of the trajectories, we demonstrate that our system converges on the correct route ID within a few minutes, even after a vehicle switches from serving one trip to the next."}],"date_published":"2019-11-28T00:00:00Z","scopus_import":"1","doi":"10.1109/ITSC.2019.8917514","status":"public","author":[{"orcid":"0000-0002-8882-5116","last_name":"Osang","full_name":"Osang, Georg F","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cook","full_name":"Cook, James","first_name":"James"},{"full_name":"Fabrikant, Alex","last_name":"Fabrikant","first_name":"Alex"},{"last_name":"Gruteser","full_name":"Gruteser, Marco","first_name":"Marco"}],"article_processing_charge":"No","publisher":"IEEE","article_number":"8917514","oa_version":"None","type":"conference","date_created":"2019-12-29T23:00:47Z","citation":{"apa":"Osang, G. F., Cook, J., Fabrikant, A., &#38; Gruteser, M. (2019). LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In <i>2019 IEEE Intelligent Transportation Systems Conference</i>. Auckland, New Zealand: IEEE. <a href=\"https://doi.org/10.1109/ITSC.2019.8917514\">https://doi.org/10.1109/ITSC.2019.8917514</a>","chicago":"Osang, Georg F, James Cook, Alex Fabrikant, and Marco Gruteser. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” In <i>2019 IEEE Intelligent Transportation Systems Conference</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/ITSC.2019.8917514\">https://doi.org/10.1109/ITSC.2019.8917514</a>.","mla":"Osang, Georg F., et al. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” <i>2019 IEEE Intelligent Transportation Systems Conference</i>, 8917514, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/ITSC.2019.8917514\">10.1109/ITSC.2019.8917514</a>.","ama":"Osang GF, Cook J, Fabrikant A, Gruteser M. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In: <i>2019 IEEE Intelligent Transportation Systems Conference</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/ITSC.2019.8917514\">10.1109/ITSC.2019.8917514</a>","short":"G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent Transportation Systems Conference, IEEE, 2019.","ieee":"G. F. Osang, J. Cook, A. Fabrikant, and M. Gruteser, “LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale,” in <i>2019 IEEE Intelligent Transportation Systems Conference</i>, Auckland, New Zealand, 2019.","ista":"Osang GF, Cook J, Fabrikant A, Gruteser M. 2019. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. 2019 IEEE Intelligent Transportation Systems Conference. ITSC: Intelligent Transportation Systems Conference, 8917514."},"quality_controlled":"1","publication_status":"published","external_id":{"isi":["000521238102050"]},"_id":"7216","conference":{"location":"Auckland, New Zealand","end_date":"2019-10-30","name":"ITSC: Intelligent Transportation Systems Conference","start_date":"2019-10-27"},"publication_identifier":{"isbn":["9781538670248"]},"isi":1,"month":"11","year":"2019","department":[{"_id":"HeEd"}],"title":"LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale"},{"quality_controlled":"1","date_created":"2020-01-05T23:00:46Z","citation":{"chicago":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2019. <a href=\"https://doi.org/10.1063/1.5138135\">https://doi.org/10.1063/1.5138135</a>.","apa":"Jaksic, V., &#38; Seiringer, R. (2019). Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5138135\">https://doi.org/10.1063/1.5138135</a>","mla":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” <i>Journal of Mathematical Physics</i>, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:<a href=\"https://doi.org/10.1063/1.5138135\">10.1063/1.5138135</a>.","short":"V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).","ista":"Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 60(12), 123504.","ieee":"V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018,” <i>Journal of Mathematical Physics</i>, vol. 60, no. 12. AIP Publishing, 2019.","ama":"Jaksic V, Seiringer R. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. <i>Journal of Mathematical Physics</i>. 2019;60(12). doi:<a href=\"https://doi.org/10.1063/1.5138135\">10.1063/1.5138135</a>"},"oa":1,"article_number":"123504","title":"Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018","date_published":"2019-12-01T00:00:00Z","intvolume":"        60","has_accepted_license":"1","publication":"Journal of Mathematical Physics","day":"01","volume":60,"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:54Z","doi":"10.1063/1.5138135","external_id":{"isi":["000505529800002"]},"publication_status":"published","_id":"7226","issue":"12","file":[{"relation":"main_file","file_id":"7244","creator":"dernst","file_name":"2019_JournalMathPhysics_Jaksic.pdf","date_created":"2020-01-07T14:59:13Z","file_size":1025015,"checksum":"bbd12ad1999a9ad7ba4d3c6f2e579c22","date_updated":"2020-07-14T12:47:54Z","access_level":"open_access","content_type":"application/pdf"}],"type":"journal_article","oa_version":"Published Version","ddc":["500"],"publisher":"AIP Publishing","article_type":"letter_note","department":[{"_id":"RoSe"}],"month":"12","year":"2019","publication_identifier":{"issn":["00222488"]},"isi":1,"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2024-02-28T13:01:45Z","status":"public","author":[{"full_name":"Jaksic, Vojkan","last_name":"Jaksic","first_name":"Vojkan"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}]},{"author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","last_name":"Koval","full_name":"Koval, Nikita"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roman","full_name":"Elizarov, Roman","last_name":"Elizarov"}],"status":"public","scopus_import":"1","abstract":[{"lang":"eng","text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) and actor models, which share data via explicit communication. These models have been known for almost half a century, and have recently had started to gain significant traction among modern programming languages. The common abstraction for communication between several processes is the channel. Although channels are similar to producer-consumer data structures, they have different semantics and support additional operations, such as the select expression. Despite their growing popularity, most known implementations of channels use lock-based data structures and can be rather inefficient.\r\n\r\nIn this paper, we present the first efficient lock-free algorithm for implementing a communication channel for CSP programming. We provide implementations and experimental results in the Kotlin and Go programming languages. Our new algorithm outperforms existing implementations on many workloads, while providing non-blocking progress guarantee. Our design can serve as an example of how to construct general communication data structures for CSP and actor models. "}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-06T14:53:59Z","department":[{"_id":"DaAl"}],"year":"2019","month":"08","isi":1,"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["978-3-0302-9399-4"]},"_id":"7228","alternative_title":["LNCS"],"publication_status":"published","external_id":{"isi":["000851061400023"]},"type":"conference","oa_version":"None","publisher":"Springer Nature","article_processing_charge":"No","doi":"10.1007/978-3-030-29400-7_23","date_published":"2019-08-13T00:00:00Z","intvolume":"     11725","volume":11725,"publication":"25th Anniversary of Euro-Par","day":"13","title":"Scalable FIFO channels for programming via communicating sequential processes","page":"317-333","conference":{"end_date":"2019-08-30","location":"Göttingen, Germany","start_date":"2019-08-26","name":"Euro-Par: European Conference on Parallel Processing"},"quality_controlled":"1","date_created":"2020-01-05T23:00:46Z","citation":{"ama":"Koval N, Alistarh D-A, Elizarov R. Scalable FIFO channels for programming via communicating sequential processes. In: <i>25th Anniversary of Euro-Par</i>. Vol 11725. Springer Nature; 2019:317-333. doi:<a href=\"https://doi.org/10.1007/978-3-030-29400-7_23\">10.1007/978-3-030-29400-7_23</a>","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par, Springer Nature, 2019, pp. 317–333.","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Scalable FIFO channels for programming via communicating sequential processes,” in <i>25th Anniversary of Euro-Par</i>, Göttingen, Germany, 2019, vol. 11725, pp. 317–333.","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Scalable FIFO channels for programming via communicating sequential processes. 25th Anniversary of Euro-Par. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11725, 317–333.","mla":"Koval, Nikita, et al. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” <i>25th Anniversary of Euro-Par</i>, vol. 11725, Springer Nature, 2019, pp. 317–33, doi:<a href=\"https://doi.org/10.1007/978-3-030-29400-7_23\">10.1007/978-3-030-29400-7_23</a>.","apa":"Koval, N., Alistarh, D.-A., &#38; Elizarov, R. (2019). Scalable FIFO channels for programming via communicating sequential processes. In <i>25th Anniversary of Euro-Par</i> (Vol. 11725, pp. 317–333). Göttingen, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-29400-7_23\">https://doi.org/10.1007/978-3-030-29400-7_23</a>","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” In <i>25th Anniversary of Euro-Par</i>, 11725:317–33. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-29400-7_23\">https://doi.org/10.1007/978-3-030-29400-7_23</a>."}},{"date_updated":"2023-09-06T14:56:00Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://arxiv.org/abs/1908.08129","open_access":"1"}],"abstract":[{"lang":"eng","text":"Simple drawings of graphs are those in which each pair of edges share at most one point, either a common endpoint or a proper crossing. In this paper we study the problem of extending a simple drawing D(G) of a graph G by inserting a set of edges from the complement of G into D(G) such that the result is a simple drawing. In the context of rectilinear drawings, the problem is trivial. For pseudolinear drawings, the existence of such an extension follows from Levi’s enlargement lemma. In contrast, we prove that deciding if a given set of edges can be inserted into a simple drawing is NP-complete. Moreover, we show that the maximization version of the problem is APX-hard. We also present a polynomial-time algorithm for deciding whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for the graph G."}],"scopus_import":"1","status":"public","author":[{"orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","last_name":"Arroyo Guevara","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M"},{"first_name":"Martin","last_name":"Derka","full_name":"Derka, Martin"},{"last_name":"Parada","full_name":"Parada, Irene","first_name":"Irene"}],"publisher":"Springer Nature","type":"conference","oa_version":"Preprint","external_id":{"isi":["000612918800018"],"arxiv":["1908.08129"]},"publication_status":"published","alternative_title":["LNCS"],"_id":"7230","publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-0303-5801-3"],"eissn":["1611-3349"]},"isi":1,"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"month":"11","year":"2019","department":[{"_id":"UlWa"}],"day":"28","publication":"27th International Symposium on Graph Drawing and Network Visualization","volume":11904,"intvolume":"     11904","date_published":"2019-11-28T00:00:00Z","doi":"10.1007/978-3-030-35802-0_18","article_processing_charge":"No","ec_funded":1,"oa":1,"citation":{"short":"A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243.","ista":"Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 11904, 230–243.","ieee":"A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,” in <i>27th International Symposium on Graph Drawing and Network Visualization</i>, Prague, Czech Republic, 2019, vol. 11904, pp. 230–243.","ama":"Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: <i>27th International Symposium on Graph Drawing and Network Visualization</i>. Vol 11904. Springer Nature; 2019:230-243. doi:<a href=\"https://doi.org/10.1007/978-3-030-35802-0_18\">10.1007/978-3-030-35802-0_18</a>","chicago":"Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple Drawings.” In <i>27th International Symposium on Graph Drawing and Network Visualization</i>, 11904:230–43. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-35802-0_18\">https://doi.org/10.1007/978-3-030-35802-0_18</a>.","apa":"Arroyo Guevara, A. M., Derka, M., &#38; Parada, I. (2019). Extending simple drawings. In <i>27th International Symposium on Graph Drawing and Network Visualization</i> (Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-35802-0_18\">https://doi.org/10.1007/978-3-030-35802-0_18</a>","mla":"Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” <i>27th International Symposium on Graph Drawing and Network Visualization</i>, vol. 11904, Springer Nature, 2019, pp. 230–43, doi:<a href=\"https://doi.org/10.1007/978-3-030-35802-0_18\">10.1007/978-3-030-35802-0_18</a>."},"date_created":"2020-01-05T23:00:47Z","quality_controlled":"1","arxiv":1,"conference":{"location":"Prague, Czech Republic","end_date":"2019-09-20","start_date":"2019-09-17","name":"GD: Graph Drawing and Network Visualization"},"page":"230-243","title":"Extending simple drawings"},{"scopus_import":"1","abstract":[{"text":"Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation for nonlinear systems with polynomial dynamics, which leverages a combination of barrier certificates. PBT has advantages over traditional time-step based methods in dealing with those nonlinear dynamical systems in which there is a large difference in speed between trajectories, producing an overapproximation that is time independent. However, the existing approach for PBT is not efficient due to the application of interval methods for enclosure-box computation, and it can only deal with continuous dynamical systems without uncertainty. In this paper, we extend the approach with the ability to handle both continuous and hybrid dynamical systems with uncertainty that can reside in parameters and/or noise. We also improve the efficiency of the method significantly, by avoiding the use of interval-based methods for the enclosure-box computation without loosing soundness. We have developed a C++ prototype implementing the proposed approach and we evaluate it on several benchmarks. The experiments show that our approach is more efficient and precise than other methods in the literature.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1907.11514","open_access":"1"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-06T14:55:15Z","author":[{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui","orcid":"0000-0002-3066-6941","last_name":"Kong","full_name":"Kong, Hui"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"last_name":"Jiang","full_name":"Jiang, Yu","first_name":"Yu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"status":"public","_id":"7231","publication_status":"published","alternative_title":["LNCS"],"external_id":{"arxiv":["1907.11514"],"isi":["000611677700008"]},"oa_version":"Preprint","type":"conference","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"month":"08","year":"2019","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"isi":1,"publication_identifier":{"isbn":["978-3-0302-9661-2"],"issn":["0302-9743"],"eissn":["1611-3349"]},"date_published":"2019-08-13T00:00:00Z","intvolume":"     11750","volume":11750,"publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","day":"13","article_processing_charge":"No","doi":"10.1007/978-3-030-29662-9_8","conference":{"location":"Amsterdam, The Netherlands","end_date":"2019-08-29","name":"FORMATS: Formal Modeling and Analysis of Timed Systems","start_date":"2019-08-27"},"quality_controlled":"1","arxiv":1,"date_created":"2020-01-05T23:00:47Z","citation":{"mla":"Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:<a href=\"https://doi.org/10.1007/978-3-030-29662-9_8\">10.1007/978-3-030-29662-9_8</a>.","chicago":"Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>, 11750:123–41. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-29662-9_8\">https://doi.org/10.1007/978-3-030-29662-9_8</a>.","apa":"Kong, H., Bartocci, E., Jiang, Y., &#38; Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i> (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-29662-9_8\">https://doi.org/10.1007/978-3-030-29662-9_8</a>","ieee":"H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 123–141.","short":"H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141.","ista":"Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11750, 123–141.","ama":"Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In: <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>. Vol 11750. Springer Nature; 2019:123-141. doi:<a href=\"https://doi.org/10.1007/978-3-030-29662-9_8\">10.1007/978-3-030-29662-9_8</a>"},"oa":1,"title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","page":"123-141"},{"citation":{"ama":"Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>. Vol 11750. Springer Nature; 2019:59-75. doi:<a href=\"https://doi.org/10.1007/978-3-030-29662-9_4\">10.1007/978-3-030-29662-9_4</a>","short":"T. Ferrere, O. Maler, D. Nickovic, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 59–75.","ieee":"T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,” in <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75.","ista":"Ferrere T, Maler O, Nickovic D. 2019. Mixed-time signal temporal logic. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Anaysis of Timed Systems, LNCS, vol. 11750, 59–75.","mla":"Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>, vol. 11750, Springer Nature, 2019, pp. 59–75, doi:<a href=\"https://doi.org/10.1007/978-3-030-29662-9_4\">10.1007/978-3-030-29662-9_4</a>.","apa":"Ferrere, T., Maler, O., &#38; Nickovic, D. (2019). Mixed-time signal temporal logic. In <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i> (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-29662-9_4\">https://doi.org/10.1007/978-3-030-29662-9_4</a>","chicago":"Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal Logic.” In <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>, 11750:59–75. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-29662-9_4\">https://doi.org/10.1007/978-3-030-29662-9_4</a>."},"date_created":"2020-01-05T23:00:48Z","conference":{"name":"FORMATS: Formal Modeling and Anaysis of Timed Systems","start_date":"2019-08-27","location":"Amsterdam, The Netherlands","end_date":"2019-08-29"},"quality_controlled":"1","page":"59-75","title":"Mixed-time signal temporal logic","volume":11750,"day":"13","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","intvolume":"     11750","date_published":"2019-08-13T00:00:00Z","doi":"10.1007/978-3-030-29662-9_4","article_processing_charge":"No","publisher":"Springer Nature","oa_version":"None","type":"conference","_id":"7232","publication_status":"published","external_id":{"isi":["000611677700004"]},"alternative_title":["LNCS"],"isi":1,"publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-0302-9661-2"],"eissn":["1611-3349"]},"year":"2019","month":"08","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"ToHe"}],"date_updated":"2023-09-06T14:57:17Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"We present Mixed-time Signal Temporal Logic (STL−MX), a specification formalism which extends STL by capturing the discrete/ continuous time duality found in many cyber-physical systems (CPS), as well as mixed-signal electronic designs. In STL−MX, properties of components with continuous dynamics are expressed in STL, while specifications of components with discrete dynamics are written in LTL. To combine the two layers, we evaluate formulas on two traces, discrete- and continuous-time, and introduce two interface operators that map signals, properties and their satisfaction signals across the two time domains. We show that STL-mx has the expressive power of STL supplemented with an implicit T-periodic clock signal. We develop and implement an algorithm for monitoring STL-mx formulas and illustrate the approach using a mixed-signal example. ","lang":"eng"}],"scopus_import":"1","author":[{"full_name":"Ferrere, Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Maler","full_name":"Maler, Oded","first_name":"Oded"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan"}],"status":"public"}]