[{"_id":"7165","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","status":"public","intvolume":" 146","oa_version":"Published Version","file":[{"file_id":"7177","relation":"main_file","checksum":"b6533c37dc8fbd803ffeca216e0a8b8a","date_created":"2019-12-13T07:34:06Z","date_updated":"2020-07-14T12:47:50Z","access_level":"open_access","file_name":"2019_Development_Guerrero.pdf","creator":"dernst","content_type":"application/pdf","file_size":7797881}],"type":"journal_article","abstract":[{"lang":"eng","text":"Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube."}],"issue":"23","publication":"Development","citation":{"chicago":"Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.176297.","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019).","mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:10.1242/dev.176297.","ieee":"P. Guerrero et al., “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” Development, vol. 146, no. 23. The Company of Biologists, 2019.","apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., & Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. The Company of Biologists. https://doi.org/10.1242/dev.176297","ista":"Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297.","ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 2019;146(23). doi:10.1242/dev.176297"},"article_type":"original","date_published":"2019-12-04T00:00:00Z","scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"No","year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"AnKi"}],"publisher":"The Company of Biologists","author":[{"last_name":"Guerrero","first_name":"Pilar","full_name":"Guerrero, Pilar"},{"full_name":"Perez-Carrasco, Ruben","last_name":"Perez-Carrasco","first_name":"Ruben"},{"full_name":"Zagórski, Marcin P","last_name":"Zagórski","first_name":"Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Page","full_name":"Page, David"},{"last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"},{"full_name":"Briscoe, James","first_name":"James","last_name":"Briscoe"},{"first_name":"Karen M.","last_name":"Page","full_name":"Page, Karen M."}],"date_created":"2019-12-10T14:39:50Z","date_updated":"2023-09-06T11:26:36Z","volume":146,"article_number":"dev176297","file_date_updated":"2020-07-14T12:47:50Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31784457"],"isi":["000507575700004"]},"quality_controlled":"1","isi":1,"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020"}],"doi":"10.1242/dev.176297","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]}},{"author":[{"first_name":"Dejan","last_name":"Ničković","full_name":"Ničković, Dejan"},{"first_name":"Xin","last_name":"Qin","full_name":"Qin, Xin"},{"full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mateis, Cristinel","first_name":"Cristinel","last_name":"Mateis"},{"first_name":"Jyotirmoy","last_name":"Deshmukh","full_name":"Deshmukh, Jyotirmoy"}],"volume":11757,"date_created":"2019-12-09T08:47:55Z","date_updated":"2023-09-06T11:24:10Z","year":"2019","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","doi":"10.1007/978-3-030-32079-9_17","conference":{"end_date":"2019-10-11","start_date":"2019-10-08","location":"Porto, Portugal","name":"RV: Runtime Verification"},"language":[{"iso":"eng"}],"external_id":{"isi":["000570006300017"]},"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030320782","9783030320799"]},"month":"10","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7159","intvolume":" 11757","status":"public","title":"Shape expressions for specifying and extracting signal features","abstract":[{"lang":"eng","text":"Cyber-physical systems (CPS) and the Internet-of-Things (IoT) result in a tremendous amount of generated, measured and recorded time-series data. Extracting temporal segments that encode patterns with useful information out of these huge amounts of data is an extremely difficult problem. We propose shape expressions as a declarative formalism for specifying, querying and extracting sophisticated temporal patterns from possibly noisy data. Shape expressions are regular expressions with arbitrary (linear, exponential, sinusoidal, etc.) shapes with parameters as atomic predicates and additional constraints on these parameters. We equip shape expressions with a novel noisy semantics that combines regular expression matching semantics with statistical regression. We characterize essential properties of the formalism and propose an efficient approximate shape expression matching procedure. We demonstrate the wide applicability of this technique on two case studies. "}],"type":"conference","alternative_title":["LNCS"],"date_published":"2019-10-01T00:00:00Z","citation":{"ama":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. Shape expressions for specifying and extracting signal features. In: 19th International Conference on Runtime Verification. Vol 11757. Springer Nature; 2019:292-309. doi:10.1007/978-3-030-32079-9_17","ista":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. 2019. Shape expressions for specifying and extracting signal features. 19th International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 11757, 292–309.","ieee":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, and J. Deshmukh, “Shape expressions for specifying and extracting signal features,” in 19th International Conference on Runtime Verification, Porto, Portugal, 2019, vol. 11757, pp. 292–309.","apa":"Ničković, D., Qin, X., Ferrere, T., Mateis, C., & Deshmukh, J. (2019). Shape expressions for specifying and extracting signal features. In 19th International Conference on Runtime Verification (Vol. 11757, pp. 292–309). Porto, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-32079-9_17","mla":"Ničković, Dejan, et al. “Shape Expressions for Specifying and Extracting Signal Features.” 19th International Conference on Runtime Verification, vol. 11757, Springer Nature, 2019, pp. 292–309, doi:10.1007/978-3-030-32079-9_17.","short":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, J. Deshmukh, in:, 19th International Conference on Runtime Verification, Springer Nature, 2019, pp. 292–309.","chicago":"Ničković, Dejan, Xin Qin, Thomas Ferrere, Cristinel Mateis, and Jyotirmoy Deshmukh. “Shape Expressions for Specifying and Extracting Signal Features.” In 19th International Conference on Runtime Verification, 11757:292–309. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-32079-9_17."},"publication":"19th International Conference on Runtime Verification","page":"292-309","article_processing_charge":"No","day":"01","scopus_import":"1"},{"month":"10","publication_identifier":{"issn":["03029743"],"isbn":["9783030317836"],"eissn":["16113349"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"oa":1,"external_id":{"isi":["000723515700027"],"arxiv":["1907.11010"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.11010"}],"language":[{"iso":"eng"}],"conference":{"name":"ATVA: Automated TEchnology for Verification and Analysis","end_date":"2019-10-31","location":"Taipei, Taiwan","start_date":"2019-10-28"},"doi":"10.1007/978-3-030-31784-3_27","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","year":"2019","date_updated":"2023-09-06T12:40:58Z","date_created":"2019-12-15T23:00:44Z","volume":11781,"author":[{"first_name":"Tomás","last_name":"Brázdil","full_name":"Brázdil, Tomás"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Kucera, Antonín","first_name":"Antonín","last_name":"Kucera"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotný","full_name":"Novotný, Petr"},{"full_name":"Velan, Dominik","last_name":"Velan","first_name":"Dominik"}],"scopus_import":"1","day":"21","article_processing_charge":"No","page":"462-478","publication":"International Symposium on Automated Technology for Verification and Analysis","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.","mla":"Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” International Symposium on Automated Technology for Verification and Analysis, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:10.1007/978-3-030-31784-3_27.","chicago":"Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In International Symposium on Automated Technology for Verification and Analysis, 11781:462–78. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31784-3_27.","ama":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: International Symposium on Automated Technology for Verification and Analysis. Vol 11781. Springer Nature; 2019:462-478. doi:10.1007/978-3-030-31784-3_27","ieee":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in International Symposium on Automated Technology for Verification and Analysis, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478.","apa":"Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., & Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In International Symposium on Automated Technology for Verification and Analysis (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-030-31784-3_27","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."},"date_published":"2019-10-21T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"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).","lang":"eng"}],"status":"public","title":"Deciding fast termination for probabilistic VASS with nondeterminism","intvolume":" 11781","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7183","oa_version":"Preprint"},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7182","ddc":["580"],"status":"public","title":"Systematic Y2H screening reveals extensive effector-complex formation","intvolume":" 10","oa_version":"Published Version","file":[{"file_name":"2019_FrontiersPlant_Alcantara.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1532505,"creator":"dernst","relation":"main_file","file_id":"7185","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-16T07:58:43Z","checksum":"995aa838aec2064d93550de82b40bbd1"}],"scopus_import":"1","day":"14","article_processing_charge":"No","has_accepted_license":"1","publication":"Frontiers in Plant Science","citation":{"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.” Frontiers in Plant Science. Frontiers, 2019. https://doi.org/10.3389/fpls.2019.01437.","mla":"Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science, vol. 10, no. 11, 1437, Frontiers, 2019, doi:10.3389/fpls.2019.01437.","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).","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.","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. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2019.01437","ieee":"A. Alcântara et al., “Systematic Y2H screening reveals extensive effector-complex formation,” Frontiers in Plant Science, vol. 10, no. 11. Frontiers, 2019.","ama":"Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 2019;10(11). doi:10.3389/fpls.2019.01437"},"article_type":"original","date_published":"2019-11-14T00:00:00Z","article_number":"1437","file_date_updated":"2020-07-14T12:47:52Z","year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Frontiers","author":[{"last_name":"Alcântara","first_name":"André","full_name":"Alcântara, André"},{"full_name":"Bosch, Jason","first_name":"Jason","last_name":"Bosch"},{"last_name":"Nazari","first_name":"Fahimeh","full_name":"Nazari, Fahimeh"},{"last_name":"Hoffmann","first_name":"Gesa","full_name":"Hoffmann, Gesa"},{"full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","last_name":"Uhse","full_name":"Uhse, Simon"},{"full_name":"Darino, Martin A.","last_name":"Darino","first_name":"Martin A."},{"full_name":"Olukayode, Toluwase","last_name":"Olukayode","first_name":"Toluwase"},{"last_name":"Reumann","first_name":"Daniel","full_name":"Reumann, Daniel"},{"full_name":"Baggaley, Laura","first_name":"Laura","last_name":"Baggaley"},{"last_name":"Djamei","first_name":"Armin","full_name":"Djamei, Armin"}],"date_updated":"2023-09-06T14:33:46Z","date_created":"2019-12-15T23:00:43Z","volume":10,"month":"11","publication_identifier":{"eissn":["1664462X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000499821700001"],"pmid":["31803201"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.3389/fpls.2019.01437","language":[{"iso":"eng"}]},{"publication_identifier":{"eissn":["20411723"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-13543-1","project":[{"grant_number":"M02379","_id":"264CBBAC-B435-11E9-9278-68D0E5697425","name":"Modeling epithelial tissue mechanics during cell invasion","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000500508100001"],"pmid":["31797871"]},"file_date_updated":"2020-07-14T12:47:52Z","article_number":"5516","volume":10,"date_updated":"2023-09-06T14:08:21Z","date_created":"2019-12-15T23:00:43Z","author":[{"full_name":"Retzer, Katarzyna","last_name":"Retzer","first_name":"Katarzyna"},{"first_name":"Maria","last_name":"Akhmanova","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1522-3162","full_name":"Akhmanova, Maria"},{"first_name":"Nataliia","last_name":"Konstantinova","full_name":"Konstantinova, Nataliia"},{"full_name":"Malínská, Kateřina","first_name":"Kateřina","last_name":"Malínská"},{"last_name":"Leitner","first_name":"Johannes","full_name":"Leitner, Johannes"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"}],"department":[{"_id":"DaSi"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2019","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","article_type":"original","citation":{"apa":"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. Springer Nature. https://doi.org/10.1038/s41467-019-13543-1","ieee":"K. Retzer et al., “Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter,” Nature Communications, vol. 10. Springer Nature, 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. Nature Communications. 2019;10. doi:10.1038/s41467-019-13543-1","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.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13543-1.","short":"K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek, C. Luschnig, Nature Communications 10 (2019).","mla":"Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications, vol. 10, 5516, Springer Nature, 2019, doi:10.1038/s41467-019-13543-1."},"publication":"Nature Communications","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"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-16T07:37:50Z","checksum":"77e8720a8e0f3091b98159f85be40893","file_id":"7184","relation":"main_file","creator":"dernst","file_size":5156533,"content_type":"application/pdf","file_name":"2019_NatureComm_Retzer.pdf","access_level":"open_access"}],"intvolume":" 10","status":"public","ddc":["570"],"title":"Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter","_id":"7180","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_published":"2019-12-01T00:00:00Z","publication":"Nature Biotechnology","citation":{"ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6","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. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6","ieee":"E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.","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.","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.","mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.","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.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6."},"article_type":"original","page":"1466-1470","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","_id":"7181","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Large multiple sequence alignments with a root-to-leaf regressive method","status":"public","intvolume":" 37","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."}],"issue":"12","type":"journal_article","doi":"10.1038/s41587-019-0333-6","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/","open_access":"1"}],"external_id":{"isi":["000500748900021"],"pmid":["31792410"]},"isi":1,"quality_controlled":"1","project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"}],"month":"12","publication_identifier":{"eissn":["15461696"],"issn":["10870156"]},"author":[{"full_name":"Garriga, Edgar","first_name":"Edgar","last_name":"Garriga"},{"first_name":"Paolo","last_name":"Di Tommaso","full_name":"Di Tommaso, Paolo"},{"full_name":"Magis, Cedrik","last_name":"Magis","first_name":"Cedrik"},{"full_name":"Erb, Ionas","last_name":"Erb","first_name":"Ionas"},{"full_name":"Mansouri, Leila","last_name":"Mansouri","first_name":"Leila"},{"first_name":"Athanasios","last_name":"Baltzis","full_name":"Baltzis, Athanasios"},{"first_name":"Hafid","last_name":"Laayouni","full_name":"Laayouni, Hafid"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"first_name":"Evan","last_name":"Floden","full_name":"Floden, Evan"},{"last_name":"Notredame","first_name":"Cedric","full_name":"Notredame, Cedric"}],"related_material":{"record":[{"id":"13059","relation":"research_data","status":"public"}]},"date_created":"2019-12-15T23:00:43Z","date_updated":"2023-09-06T14:32:52Z","volume":37,"year":"2019","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"ec_funded":1},{"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000508156800001"],"pmid":["31736464"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.51381","month":"11","publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"SiHi"}],"year":"2019","pmid":1,"date_created":"2019-12-22T23:00:42Z","date_updated":"2023-09-06T14:38:39Z","volume":8,"author":[{"first_name":"Alfredo","last_name":"Llorca","full_name":"Llorca, Alfredo"},{"full_name":"Ciceri, Gabriele","first_name":"Gabriele","last_name":"Ciceri"},{"orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","first_name":"Robert J","full_name":"Beattie, Robert J"},{"last_name":"Wong","first_name":"Fong Kuan","full_name":"Wong, Fong Kuan"},{"last_name":"Diana","first_name":"Giovanni","full_name":"Diana, Giovanni"},{"full_name":"Serafeimidou-Pouliou, Eleni","last_name":"Serafeimidou-Pouliou","first_name":"Eleni"},{"full_name":"Fernández-Otero, Marian","first_name":"Marian","last_name":"Fernández-Otero"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"full_name":"Arnold, Sebastian J.","last_name":"Arnold","first_name":"Sebastian J."},{"last_name":"Meyer","first_name":"Martin","full_name":"Meyer, Martin"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Miguel","last_name":"Maravall","full_name":"Maravall, Miguel"},{"last_name":"Marín","first_name":"Oscar","full_name":"Marín, Oscar"}],"article_number":"e51381","file_date_updated":"2020-07-14T12:47:53Z","ec_funded":1,"article_type":"original","publication":"eLife","citation":{"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).","mla":"Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife, vol. 8, e51381, eLife Sciences Publications, 2019, doi:10.7554/eLife.51381.","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.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.51381.","ama":"Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 2019;8. doi:10.7554/eLife.51381","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. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51381","ieee":"A. Llorca et al., “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” eLife, vol. 8. eLife Sciences Publications, 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."},"date_published":"2019-11-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","status":"public","ddc":["570"],"title":"A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture","intvolume":" 8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7202","file":[{"date_created":"2020-02-18T15:19:26Z","date_updated":"2020-07-14T12:47:53Z","checksum":"b460ecc33e1a68265e7adea775021f3a","file_id":"7503","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2960543,"file_name":"2019_eLife_Llorca.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","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."}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7179","intvolume":" 33","ddc":["571","599"],"title":"Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses","status":"public","oa_version":"Submitted Version","file":[{"file_size":4766789,"content_type":"application/pdf","creator":"shigemot","access_level":"open_access","file_name":"Klotz et al 2019 EMBO Reports.pdf","checksum":"79e3b72481dc32489911121cf3b7d8d0","success":1,"date_updated":"2020-12-06T17:30:09Z","date_created":"2020-12-06T17:30:09Z","relation":"main_file","file_id":"8922"}],"type":"journal_article","issue":"12","abstract":[{"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.","lang":"eng"}],"citation":{"apa":"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. FASEB. https://doi.org/10.1096/fj.201901543R","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,” FASEB Journal, vol. 33, no. 12. FASEB, pp. 13734–13746, 2019.","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.","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. FASEB Journal. 2019;33(12):13734-13746. doi:10.1096/fj.201901543R","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.” FASEB Journal. FASEB, 2019. https://doi.org/10.1096/fj.201901543R.","short":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz, FASEB Journal 33 (2019) 13734–13746.","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.” FASEB Journal, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:10.1096/fj.201901543R."},"publication":"FASEB Journal","page":"13734-13746","article_type":"original","date_published":"2019-12-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","pmid":1,"year":"2019","publisher":"FASEB","department":[{"_id":"RySh"}],"publication_status":"published","author":[{"full_name":"Klotz, Lisa","first_name":"Lisa","last_name":"Klotz"},{"full_name":"Wendler, Olaf","last_name":"Wendler","first_name":"Olaf"},{"first_name":"Renato","last_name":"Frischknecht","full_name":"Frischknecht, Renato"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"full_name":"Schulze, Holger","last_name":"Schulze","first_name":"Holger"},{"full_name":"Enz, Ralf","last_name":"Enz","first_name":"Ralf"}],"volume":33,"date_updated":"2023-09-06T14:34:36Z","date_created":"2019-12-15T23:00:42Z","file_date_updated":"2020-12-06T17:30:09Z","oa":1,"external_id":{"pmid":["31585509"],"isi":["000507466100054"]},"quality_controlled":"1","isi":1,"doi":"10.1096/fj.201901543R","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15306860"]},"month":"12"},{"isi":1,"quality_controlled":"1","project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"external_id":{"arxiv":["1802.08021"],"isi":["000545976800011"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1802.08021","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"name":"SC: Conference for High Performance Computing, Networking, Storage and Analysis","end_date":"2019-11-19","start_date":"2019-11-17","location":"Denver, CO, Unites States"},"doi":"10.1145/3295500.3356222","month":"11","publication_identifier":{"issn":["21674329"],"isbn":["9781450362290"],"eissn":["21674337"]},"publication_status":"published","publisher":"ACM","department":[{"_id":"DaAl"}],"year":"2019","date_updated":"2023-09-06T14:37:55Z","date_created":"2019-12-22T23:00:42Z","author":[{"last_name":"Renggli","first_name":"Cedric","full_name":"Renggli, Cedric"},{"first_name":"Saleh","last_name":"Ashkboos","id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A","full_name":"Ashkboos, Saleh"},{"last_name":"Aghagolzadeh","first_name":"Mehdi","full_name":"Aghagolzadeh, Mehdi"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"}],"article_number":"a11","ec_funded":1,"publication":"International Conference for High Performance Computing, Networking, Storage and Analysis, SC","citation":{"chicago":"Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM, 2019. https://doi.org/10.1145/3295500.3356222.","mla":"Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” International Conference for High Performance Computing, Networking, Storage and Analysis, SC, a11, ACM, 2019, doi:10.1145/3295500.3356222.","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.","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.","apa":"Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., & Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. Denver, CO, Unites States: ACM. https://doi.org/10.1145/3295500.3356222","ieee":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in International Conference for High Performance Computing, Networking, Storage and Analysis, SC, 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: International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM; 2019. doi:10.1145/3295500.3356222"},"date_published":"2019-11-17T00:00:00Z","scopus_import":"1","day":"17","article_processing_charge":"No","status":"public","title":"SparCML: High-performance sparse communication for machine learning","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7201","oa_version":"Preprint","type":"conference","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"}]},{"license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"lang":"eng","text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females."}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2023-05-23T16:36:27Z","date_updated":"2023-09-06T14:48:57Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7205"}]},"author":[{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Zagrodzka, Zuzanna","first_name":"Zuzanna","last_name":"Zagrodzka"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"department":[{"_id":"NiBa"}],"publisher":"Dryad","ddc":["570"],"status":"public","title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","_id":"13067","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","article_processing_charge":"No","month":"12","day":"02","date_published":"2019-12-02T00:00:00Z","doi":"10.5061/DRYAD.TB2RBNZWK","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019)."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.tb2rbnzwk","open_access":"1"}]},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"_id":"7214","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["570"],"title":"Recovering rearranged cancer chromosomes from karyotype graphs","intvolume":" 20","file":[{"access_level":"open_access","file_name":"2019_BMCBioinfo_Aganezov.pdf","creator":"dernst","file_size":1917374,"content_type":"application/pdf","file_id":"7221","relation":"main_file","checksum":"7a30357efdcf8f66587ed495c0927724","date_created":"2020-01-02T16:10:58Z","date_updated":"2020-07-14T12:47:54Z"}],"oa_version":"Published Version","scopus_import":"1","day":"17","article_processing_charge":"No","has_accepted_license":"1","publication":"BMC Bioinformatics","citation":{"ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics, vol. 20. BMC, 2019.","apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. BMC. https://doi.org/10.1186/s12859-019-3208-4","ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20. doi:10.1186/s12859-019-3208-4","chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4.","mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4.","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019)."},"article_type":"original","date_published":"2019-12-17T00:00:00Z","article_number":"641","file_date_updated":"2020-07-14T12:47:54Z","year":"2019","publication_status":"published","publisher":"BMC","department":[{"_id":"DaAl"}],"author":[{"first_name":"Sergey","last_name":"Aganezov","full_name":"Aganezov, Sergey"},{"last_name":"Zban","first_name":"Ilya","full_name":"Zban, Ilya"},{"id":"2980135A-F248-11E8-B48F-1D18A9856A87","last_name":"Aksenov","first_name":"Vitalii","full_name":"Aksenov, Vitalii"},{"full_name":"Alexeev, Nikita","first_name":"Nikita","last_name":"Alexeev"},{"full_name":"Schatz, Michael C.","first_name":"Michael C.","last_name":"Schatz"}],"date_created":"2019-12-29T23:00:46Z","date_updated":"2023-09-06T14:51:06Z","volume":20,"month":"12","publication_identifier":{"eissn":["14712105"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000511618800007"]},"isi":1,"quality_controlled":"1","doi":"10.1186/s12859-019-3208-4","language":[{"iso":"eng"}]},{"intvolume":" 6","title":"Frontiers in microfluidics, a teaching resource review","ddc":["620"],"status":"public","_id":"7225","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7243","checksum":"80f1499e2a4caccdf3aa54b137fd99a0","date_created":"2020-01-07T14:49:59Z","date_updated":"2020-07-14T12:47:54Z","access_level":"open_access","file_name":"2019_Bioengineering_Merrin.pdf","file_size":2660780,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"This is a literature teaching resource review for biologically inspired microfluidics courses\r\nor exploring the diverse applications of microfluidics. The structure is around key papers and model\r\norganisms. While courses gradually change over time, a focus remains on understanding how\r\nmicrofluidics has developed as well as what it can and cannot do for researchers. As a primary\r\nstarting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof applications are discussed using model prokaryotic and eukaryotic organisms from the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics can still be used effectively for specific applications."}],"article_type":"review","citation":{"apa":"Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review. Bioengineering. MDPI. https://doi.org/10.3390/bioengineering6040109","ieee":"J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering, vol. 6, no. 4. MDPI, 2019.","ista":"Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering. 6(4), 109.","ama":"Merrin J. Frontiers in microfluidics, a teaching resource review. Bioengineering. 2019;6(4). doi:10.3390/bioengineering6040109","chicago":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109.","short":"J. Merrin, Bioengineering 6 (2019).","mla":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering, vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109."},"publication":"Bioengineering","date_published":"2019-12-03T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"03","publisher":"MDPI","department":[{"_id":"NanoFab"}],"publication_status":"published","pmid":1,"year":"2019","volume":6,"date_created":"2020-01-05T23:00:45Z","date_updated":"2023-09-06T14:52:49Z","author":[{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack"}],"article_number":"109","file_date_updated":"2020-07-14T12:47:54Z","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31816954"],"isi":["000505590000024"]},"language":[{"iso":"eng"}],"doi":"10.3390/bioengineering6040109","publication_identifier":{"eissn":["23065354"]},"month":"12"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7228","intvolume":" 11725","title":"Scalable FIFO channels for programming via communicating sequential processes","status":"public","oa_version":"None","type":"conference","alternative_title":["LNCS"],"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. "}],"citation":{"ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Scalable FIFO channels for programming via communicating sequential processes,” in 25th Anniversary of Euro-Par, Göttingen, Germany, 2019, vol. 11725, pp. 317–333.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Scalable FIFO channels for programming via communicating sequential processes. In 25th Anniversary of Euro-Par (Vol. 11725, pp. 317–333). Göttingen, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-29400-7_23","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.","ama":"Koval N, Alistarh D-A, Elizarov R. Scalable FIFO channels for programming via communicating sequential processes. In: 25th Anniversary of Euro-Par. Vol 11725. Springer Nature; 2019:317-333. doi:10.1007/978-3-030-29400-7_23","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” In 25th Anniversary of Euro-Par, 11725:317–33. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29400-7_23.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par, Springer Nature, 2019, pp. 317–333.","mla":"Koval, Nikita, et al. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” 25th Anniversary of Euro-Par, vol. 11725, Springer Nature, 2019, pp. 317–33, doi:10.1007/978-3-030-29400-7_23."},"publication":"25th Anniversary of Euro-Par","page":"317-333","date_published":"2019-08-13T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"13","year":"2019","publisher":"Springer Nature","department":[{"_id":"DaAl"}],"publication_status":"published","author":[{"first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"last_name":"Elizarov","first_name":"Roman","full_name":"Elizarov, Roman"}],"volume":11725,"date_created":"2020-01-05T23:00:46Z","date_updated":"2023-09-06T14:53:59Z","external_id":{"isi":["000851061400023"]},"isi":1,"quality_controlled":"1","doi":"10.1007/978-3-030-29400-7_23","conference":{"name":"Euro-Par: European Conference on Parallel Processing","end_date":"2019-08-30","start_date":"2019-08-26","location":"Göttingen, Germany"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9399-4"]},"month":"08"},{"abstract":[{"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.","lang":"eng"}],"article_number":"8917514","type":"conference","date_updated":"2023-09-06T14:50:28Z","date_created":"2019-12-29T23:00:47Z","oa_version":"None","author":[{"full_name":"Osang, Georg F","last_name":"Osang","first_name":"Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cook, James","first_name":"James","last_name":"Cook"},{"first_name":"Alex","last_name":"Fabrikant","full_name":"Fabrikant, Alex"},{"full_name":"Gruteser, Marco","first_name":"Marco","last_name":"Gruteser"}],"publication_status":"published","title":"LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale","status":"public","department":[{"_id":"HeEd"}],"publisher":"IEEE","_id":"7216","year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"11","day":"28","publication_identifier":{"isbn":["9781538670248"]},"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"conference":{"location":"Auckland, New Zealand","start_date":"2019-10-27","end_date":"2019-10-30","name":"ITSC: Intelligent Transportation Systems Conference"},"doi":"10.1109/ITSC.2019.8917514","date_published":"2019-11-28T00:00:00Z","isi":1,"quality_controlled":"1","publication":"2019 IEEE Intelligent Transportation Systems Conference","external_id":{"isi":["000521238102050"]},"citation":{"ama":"Osang GF, Cook J, Fabrikant A, Gruteser M. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In: 2019 IEEE Intelligent Transportation Systems Conference. IEEE; 2019. doi:10.1109/ITSC.2019.8917514","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.","apa":"Osang, G. F., Cook, J., Fabrikant, A., & Gruteser, M. (2019). LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In 2019 IEEE Intelligent Transportation Systems Conference. Auckland, New Zealand: IEEE. https://doi.org/10.1109/ITSC.2019.8917514","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 2019 IEEE Intelligent Transportation Systems Conference, Auckland, New Zealand, 2019.","mla":"Osang, Georg F., et al. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” 2019 IEEE Intelligent Transportation Systems Conference, 8917514, IEEE, 2019, doi:10.1109/ITSC.2019.8917514.","short":"G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent Transportation Systems Conference, IEEE, 2019.","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 2019 IEEE Intelligent Transportation Systems Conference. IEEE, 2019. https://doi.org/10.1109/ITSC.2019.8917514."}},{"author":[{"last_name":"Kong","first_name":"Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"full_name":"Jiang, Yu","last_name":"Jiang","first_name":"Yu"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"}],"date_created":"2020-01-05T23:00:47Z","date_updated":"2023-09-06T14:55:15Z","volume":11750,"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"month":"08","publication_identifier":{"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"],"issn":["0302-9743"]},"conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","location":"Amsterdam, The Netherlands","start_date":"2019-08-27","end_date":"2019-08-29"},"doi":"10.1007/978-3-030-29662-9_8","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000611677700008"],"arxiv":["1907.11514"]},"main_file_link":[{"url":"https://arxiv.org/abs/1907.11514","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"abstract":[{"lang":"eng","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."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7231","title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","status":"public","intvolume":" 11750","day":"13","article_processing_charge":"No","scopus_import":"1","date_published":"2019-08-13T00:00:00Z","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","citation":{"chicago":"Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8.","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.","mla":"Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8.","apa":"Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8","ieee":"H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, 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: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:123-141. doi:10.1007/978-3-030-29662-9_8"},"page":"123-141"},{"abstract":[{"lang":"eng","text":"Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal domain (IRE1LD) that favours the latter's monomeric inactive state and loss of ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations is presently lacking. We report that enforced loading of endogenous BiP onto endogenous IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent with active destabilisation of the IRE1LD dimer. Together, these observations support a competition model whereby waning ER stress passively partitions ERdj4 and BiP to IRE1LD to initiate active repression of UPR signalling."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"8777","date_created":"2020-11-19T11:37:41Z","date_updated":"2020-11-19T11:37:41Z","checksum":"29fcbcd8c1fc7f11a596ed7f14ea1c82","success":1,"file_name":"2019_eLife_AminWetzel.pdf","access_level":"open_access","file_size":4817384,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"7340","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 8","ddc":["570"],"title":"Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR","status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"24","scopus_import":"1","date_published":"2019-12-24T00:00:00Z","citation":{"chicago":"Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer, and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.50793.","mla":"Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife, vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793.","short":"N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).","ista":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 8, e50793.","apa":"Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019). Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.50793","ieee":"N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications, 2019.","ama":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793"},"publication":"eLife","article_type":"original","file_date_updated":"2020-11-19T11:37:41Z","article_number":"e50793","author":[{"full_name":"Amin-Wetzel, Niko Paresh","first_name":"Niko Paresh","last_name":"Amin-Wetzel","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425"},{"first_name":"Lisa","last_name":"Neidhardt","full_name":"Neidhardt, Lisa"},{"full_name":"Yan, Yahui","last_name":"Yan","first_name":"Yahui"},{"full_name":"Mayer, Matthias P.","last_name":"Mayer","first_name":"Matthias P."},{"first_name":"David","last_name":"Ron","full_name":"Ron, David"}],"volume":8,"date_updated":"2023-09-06T14:58:02Z","date_created":"2020-01-19T23:00:39Z","pmid":1,"year":"2019","acknowledgement":"We thank the CIMR flow cytometry core facility team (Reiner Schulte, Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington lab for access to the Octet machine, Steffen Preissler for advice on data interpretation, Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments.","department":[{"_id":"MaDe"}],"publisher":"eLife Sciences Publications","publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"month":"12","doi":"10.7554/eLife.50793","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31873072"],"isi":["000512303700001"]},"quality_controlled":"1","isi":1},{"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1063/1.5064867","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.09364"}],"external_id":{"isi":["000458109300009"],"arxiv":["1708.09364"]},"oa":1,"article_number":"054108","volume":150,"date_created":"2020-01-30T10:34:36Z","date_updated":"2023-09-06T14:59:28Z","author":[{"full_name":"Sokolowski, Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","first_name":"Thomas R","last_name":"Sokolowski"},{"last_name":"Paijmans","first_name":"Joris","full_name":"Paijmans, Joris"},{"full_name":"Bossen, Laurens","last_name":"Bossen","first_name":"Laurens"},{"last_name":"Miedema","first_name":"Thomas","full_name":"Miedema, Thomas"},{"full_name":"Wehrens, Martijn","first_name":"Martijn","last_name":"Wehrens"},{"full_name":"Becker, Nils B.","first_name":"Nils B.","last_name":"Becker"},{"last_name":"Kaizu","first_name":"Kazunari","full_name":"Kaizu, Kazunari"},{"full_name":"Takahashi, Koichi","last_name":"Takahashi","first_name":"Koichi"},{"full_name":"Dogterom, Marileen","first_name":"Marileen","last_name":"Dogterom"},{"first_name":"Pieter Rein","last_name":"ten Wolde","full_name":"ten Wolde, Pieter Rein"}],"publisher":"AIP Publishing","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2019","article_processing_charge":"No","day":"07","date_published":"2019-02-07T00:00:00Z","article_type":"original","citation":{"apa":"Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5064867","ieee":"T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.","ista":"Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal of Chemical Physics. 150(5), 054108.","ama":"Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867","chicago":"Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.","short":"T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019).","mla":"Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867."},"publication":"The Journal of Chemical Physics","issue":"5","abstract":[{"lang":"eng","text":"Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 150","title":"eGFRD in all dimensions","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7422"},{"ec_funded":1,"date_created":"2020-01-05T23:00:47Z","date_updated":"2023-09-06T14:56:00Z","volume":11904,"author":[{"full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","last_name":"Arroyo Guevara","first_name":"Alan M"},{"full_name":"Derka, Martin","last_name":"Derka","first_name":"Martin"},{"full_name":"Parada, Irene","first_name":"Irene","last_name":"Parada"}],"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","year":"2019","month":"11","publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-0303-5801-3"],"eissn":["1611-3349"]},"language":[{"iso":"eng"}],"conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2019-09-20","start_date":"2019-09-17","location":"Prague, Czech Republic"},"doi":"10.1007/978-3-030-35802-0_18","isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000612918800018"],"arxiv":["1908.08129"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1908.08129","open_access":"1"}],"abstract":[{"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.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","status":"public","title":"Extending simple drawings","intvolume":" 11904","_id":"7230","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"28","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-28T00:00:00Z","page":"230-243","publication":"27th International Symposium on Graph Drawing and Network Visualization","citation":{"ama":"Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: 27th International Symposium on Graph Drawing and Network Visualization. Vol 11904. Springer Nature; 2019:230-243. doi:10.1007/978-3-030-35802-0_18","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.","apa":"Arroyo Guevara, A. M., Derka, M., & Parada, I. (2019). Extending simple drawings. In 27th International Symposium on Graph Drawing and Network Visualization (Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-35802-0_18","ieee":"A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,” in 27th International Symposium on Graph Drawing and Network Visualization, Prague, Czech Republic, 2019, vol. 11904, pp. 230–243.","mla":"Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” 27th International Symposium on Graph Drawing and Network Visualization, vol. 11904, Springer Nature, 2019, pp. 230–43, doi:10.1007/978-3-030-35802-0_18.","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.","chicago":"Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple Drawings.” In 27th International Symposium on Graph Drawing and Network Visualization, 11904:230–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-35802-0_18."}},{"month":"08","publication_identifier":{"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2019-08-29","start_date":"2019-08-27","location":"Amsterdam, The Netherlands","name":"FORMATS: Formal Modeling and Anaysis of Timed Systems"},"doi":"10.1007/978-3-030-29662-9_4","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"external_id":{"isi":["000611677700004"]},"date_created":"2020-01-05T23:00:48Z","date_updated":"2023-09-06T14:57:17Z","volume":11750,"author":[{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"},{"full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"year":"2019","day":"13","article_processing_charge":"No","scopus_import":"1","date_published":"2019-08-13T00:00:00Z","page":"59-75","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","citation":{"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.","mla":"Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 59–75, doi:10.1007/978-3-030-29662-9_4.","chicago":"Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal Logic.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:59–75. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_4.","ama":"Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:59-75. doi:10.1007/978-3-030-29662-9_4","ieee":"T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75.","apa":"Ferrere, T., Maler, O., & Nickovic, D. (2019). Mixed-time signal temporal logic. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_4","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."},"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"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"None","status":"public","title":"Mixed-time signal temporal logic","intvolume":" 11750","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7232"},{"department":[{"_id":"MiSi"}],"publisher":"The Company of Biologists","publication_status":"published","pmid":1,"year":"2019","volume":132,"date_created":"2020-01-30T10:31:42Z","date_updated":"2023-09-06T15:01:00Z","author":[{"first_name":"Pranshu","last_name":"Sahgal","full_name":"Sahgal, Pranshu"},{"full_name":"Alanko, Jonna H","last_name":"Alanko","first_name":"Jonna H","orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Icha, Jaroslav","first_name":"Jaroslav","last_name":"Icha"},{"full_name":"Paatero, Ilkka","last_name":"Paatero","first_name":"Ilkka"},{"full_name":"Hamidi, Hellyeh","last_name":"Hamidi","first_name":"Hellyeh"},{"first_name":"Antti","last_name":"Arjonen","full_name":"Arjonen, Antti"},{"full_name":"Pietilä, Mika","last_name":"Pietilä","first_name":"Mika"},{"first_name":"Anne","last_name":"Rokka","full_name":"Rokka, Anne"},{"last_name":"Ivaska","first_name":"Johanna","full_name":"Ivaska, Johanna"}],"article_number":"jcs233387","isi":1,"quality_controlled":"1","external_id":{"pmid":["31076515"],"isi":["000473327900017"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/jcs.233387"}],"language":[{"iso":"eng"}],"doi":"10.1242/jcs.233387","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"month":"06","intvolume":" 132","status":"public","title":"GGA2 and RAB13 promote activity-dependent β1-integrin recycling","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7420","oa_version":"Published Version","type":"journal_article","issue":"11","abstract":[{"text":"β1-integrins mediate cell–matrix interactions and their trafficking is important in the dynamic regulation of cell adhesion, migration and malignant processes, including cancer cell invasion. Here, we employ an RNAi screen to characterize regulators of integrin traffic and identify the association of Golgi-localized gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2 limits active β1-integrin levels in focal adhesions and decreases cancer cell migration and invasion, which is in agreement with its ability to regulate the dynamics of active integrins. By using the proximity-dependent biotin identification (BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10, as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular accumulation of active β1-integrin, and reduces integrin activity in focal adhesions and cell migration similarly to GGA2 depletion, indicating that both facilitate active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic.","lang":"eng"}],"article_type":"original","citation":{"short":"P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä, A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019).","mla":"Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science, vol. 132, no. 11, jcs233387, The Company of Biologists, 2019, doi:10.1242/jcs.233387.","chicago":"Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science. The Company of Biologists, 2019. https://doi.org/10.1242/jcs.233387.","ama":"Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 2019;132(11). doi:10.1242/jcs.233387","ieee":"P. Sahgal et al., “GGA2 and RAB13 promote activity-dependent β1-integrin recycling,” Journal of Cell Science, vol. 132, no. 11. The Company of Biologists, 2019.","apa":"Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A., … Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.233387","ista":"Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 132(11), jcs233387."},"publication":"Journal of Cell Science","date_published":"2019-06-07T00:00:00Z","article_processing_charge":"No","day":"07"}]