[{"publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"RP acknowledges the Department of Science and Technology, India for the support through the DST-INSPIRE Faculty Award (DST/INSPIRE/04/2015/001939). This work was supported by the Engineering and Physical Sciences Research Council (EPSRC), United Kingdom (Grant numbers EP/J018295/1, EP/J018392/1, EP/N014391/1). The contribution of RP was also supported by the later Grant. This work was generously supported by the Welcome Trust Institutional Strategic Support Award (204909/Z/16/Z) too. The contribution of MG was supported by the EPSRC via EP/N014391/1 and a Wellcome Trust Institutional Strategic Support Award (WT105618MA). The contribution of YA was generously supported by the Wellcome Trust Institutional Strategic Support Award (WT105618MA).","date_published":"2021-01-26T00:00:00Z","doi":"10.1038/s41598-020-80507-7","date_created":"2021-02-07T23:01:12Z","has_accepted_license":"1","year":"2021","day":"26","publication":"Scientific Reports","article_number":"2204","author":[{"first_name":"Rakesh","full_name":"Pandey, Rakesh","last_name":"Pandey"},{"full_name":"Al-Nuaimi, Yusur","last_name":"Al-Nuaimi","first_name":"Yusur"},{"last_name":"Mishra","full_name":"Mishra, Rajiv Kumar","first_name":"Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sarah K.","full_name":"Spurgeon, Sarah K.","last_name":"Spurgeon"},{"full_name":"Goodfellow, Marc","last_name":"Goodfellow","first_name":"Marc"}],"article_processing_charge":"No","title":"Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis","citation":{"ista":"Pandey R, Al-Nuaimi Y, Mishra RK, Spurgeon SK, Goodfellow M. 2021. Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. Scientific Reports. 11, 2204.","chicago":"Pandey, Rakesh, Yusur Al-Nuaimi, Rajiv Kumar Mishra, Sarah K. Spurgeon, and Marc Goodfellow. “Role of Subnetworks Mediated by TNF α, IL-23/IL-17 and IL-15 in a Network Involved in the Pathogenesis of Psoriasis.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-020-80507-7.","ieee":"R. Pandey, Y. Al-Nuaimi, R. K. Mishra, S. K. Spurgeon, and M. Goodfellow, “Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis,” Scientific Reports, vol. 11. Springer Nature, 2021.","short":"R. Pandey, Y. Al-Nuaimi, R.K. Mishra, S.K. Spurgeon, M. Goodfellow, Scientific Reports 11 (2021).","apa":"Pandey, R., Al-Nuaimi, Y., Mishra, R. K., Spurgeon, S. K., & Goodfellow, M. (2021). Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-80507-7","ama":"Pandey R, Al-Nuaimi Y, Mishra RK, Spurgeon SK, Goodfellow M. Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. Scientific Reports. 2021;11. doi:10.1038/s41598-020-80507-7","mla":"Pandey, Rakesh, et al. “Role of Subnetworks Mediated by TNF α, IL-23/IL-17 and IL-15 in a Network Involved in the Pathogenesis of Psoriasis.” Scientific Reports, vol. 11, 2204, Springer Nature, 2021, doi:10.1038/s41598-020-80507-7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","month":"01","intvolume":" 11","abstract":[{"lang":"eng","text":"Psoriasis is a chronic inflammatory skin disease clinically characterized by the appearance of red colored, well-demarcated plaques with thickened skin and with silvery scales. Recent studies have established the involvement of a complex signalling network of interactions between cytokines, immune cells and skin cells called keratinocytes. Keratinocytes form the cells of the outermost layer of the skin (epidermis). Visible plaques in psoriasis are developed due to the fast proliferation and unusual differentiation of keratinocyte cells. Despite that, the exact mechanism of the appearance of these plaques in the cytokine-immune cell network is not clear. A mathematical model embodying interactions between key immune cells believed to be involved in psoriasis, keratinocytes and relevant cytokines has been developed. The complex network formed of these interactions poses several challenges. Here, we choose to study subnetworks of this complex network and initially focus on interactions involving TNFα, IL-23/IL-17, and IL-15. These are chosen based on known evidence of their therapeutic efficacy. In addition, we explore the role of IL-15 in the pathogenesis of psoriasis and its potential as a future drug target for a novel treatment option. We perform steady state analyses for these subnetworks and demonstrate that the interactions between cells, driven by cytokines could cause the emergence of a psoriasis state (hyper-proliferation of keratinocytes) when levels of TNFα, IL-23/IL-17 or IL-15 are increased. The model results explain and support the clinical potentiality of anti-cytokine treatments. Interestingly, our results suggest different dynamic scenarios underpin the pathogenesis of psoriasis, depending upon the dominant cytokines of subnetworks. We observed that the increase in the level of IL-23/IL-17 and IL-15 could lead to psoriasis via a bistable route, whereas an increase in the level of TNFα would lead to a monotonic and gradual disease progression. Further, we demonstrate how this insight, bistability, could be exploited to improve the current therapies and develop novel treatment strategies for psoriasis."}],"oa_version":"Published Version","volume":11,"publication_identifier":{"eissn":["20452322"]},"publication_status":"published","file":[{"date_created":"2021-02-09T07:33:23Z","file_name":"2021_ScientificReports_Pandey.pdf","creator":"dernst","date_updated":"2021-02-09T07:33:23Z","file_size":2885056,"file_id":"9106","checksum":"e8a68df48750712671f5c47b0228e531","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9097","department":[{"_id":"PeJo"}],"file_date_updated":"2021-02-09T07:33:23Z","date_updated":"2022-08-19T07:22:23Z","ddc":["570"]},{"citation":{"ama":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-95025-3","apa":"Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3","ieee":"S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.","short":"S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).","mla":"Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.","ista":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729.","chicago":"Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-95025-3."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["34330988"],"isi":["000683329100001"]},"article_processing_charge":"Yes","author":[{"last_name":"Rella","full_name":"Rella, Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","first_name":"Simon"},{"first_name":"Yuliya A.","full_name":"Kulikova, Yuliya A.","last_name":"Kulikova"},{"first_name":"Emmanouil T.","full_name":"Dermitzakis, Emmanouil T.","last_name":"Dermitzakis"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"}],"title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","article_number":"15729","project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209"}],"year":"2021","has_accepted_license":"1","isi":1,"publication":"Scientific Reports","day":"30","date_created":"2021-08-15T22:01:26Z","doi":"10.1038/s41598-021-95025-3","date_published":"2021-07-30T00:00:00Z","acknowledgement":"We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_updated":"2023-08-11T10:42:58Z","ddc":["570","610"],"department":[{"_id":"FyKo"}],"file_date_updated":"2021-08-16T11:36:49Z","_id":"9905","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["20452322"]},"language":[{"iso":"eng"}],"file":[{"creator":"asandaue","date_updated":"2021-08-16T11:36:49Z","file_size":3432001,"date_created":"2021-08-16T11:36:49Z","file_name":"2021_ScientificReports_Rella.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9927","checksum":"ac86892ed17e6724c7251844da5cef5c","success":1}],"ec_funded":1,"issue":"1","related_material":{"link":[{"description":"News on IST Website","url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/","relation":"press_release"}]},"volume":11,"abstract":[{"text":"Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 11","month":"07"},{"article_number":"2259","citation":{"ista":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, Cardona C, Martín-Rufián M, Sialana FJ, Castilla L, Bae N, Lobo C, Peñalver A, García-Frutos M, Carro D, Enrique V, Paz JC, Mirmira RG, Gutiérrez A, Alonso FJ, Segura JA, Matés JM, Lubec G, Márquez J. 2020. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 10(1), 2259.","chicago":"López De La Oliva, Amada R., José A. Campos-Sandoval, María C. Gómez-García, Carolina Cardona, Mercedes Martín-Rufián, Fernando J. Sialana, Laura Castilla, et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-58264-4.","ama":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, et al. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-58264-4","apa":"López De La Oliva, A. R., Campos-Sandoval, J. A., Gómez-García, M. C., Cardona, C., Martín-Rufián, M., Sialana, F. J., … Márquez, J. (2020). Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-58264-4","short":"A.R. López De La Oliva, J.A. Campos-Sandoval, M.C. Gómez-García, C. Cardona, M. Martín-Rufián, F.J. Sialana, L. Castilla, N. Bae, C. Lobo, A. Peñalver, M. García-Frutos, D. Carro, V. Enrique, J.C. Paz, R.G. Mirmira, A. Gutiérrez, F.J. Alonso, J.A. Segura, J.M. Matés, G. Lubec, J. Márquez, Scientific Reports 10 (2020).","ieee":"A. R. López De La Oliva et al., “Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation,” Scientific reports, vol. 10, no. 1. Springer Nature, 2020.","mla":"López De La Oliva, Amada R., et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” Scientific Reports, vol. 10, no. 1, 2259, Springer Nature, 2020, doi:10.1038/s41598-020-58264-4."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"López De La Oliva, Amada R.","last_name":"López De La Oliva","first_name":"Amada R."},{"first_name":"José A.","full_name":"Campos-Sandoval, José A.","last_name":"Campos-Sandoval"},{"first_name":"María C.","last_name":"Gómez-García","full_name":"Gómez-García, María C."},{"first_name":"Carolina","full_name":"Cardona, Carolina","last_name":"Cardona"},{"first_name":"Mercedes","last_name":"Martín-Rufián","full_name":"Martín-Rufián, Mercedes"},{"last_name":"Sialana","full_name":"Sialana, Fernando J.","first_name":"Fernando J."},{"full_name":"Castilla, Laura","last_name":"Castilla","first_name":"Laura"},{"first_name":"Narkhyun","id":"3A5F7CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Bae","full_name":"Bae, Narkhyun"},{"first_name":"Carolina","last_name":"Lobo","full_name":"Lobo, Carolina"},{"last_name":"Peñalver","full_name":"Peñalver, Ana","first_name":"Ana"},{"first_name":"Marina","last_name":"García-Frutos","full_name":"García-Frutos, Marina"},{"last_name":"Carro","full_name":"Carro, David","first_name":"David"},{"first_name":"Victoria","full_name":"Enrique, Victoria","last_name":"Enrique"},{"last_name":"Paz","full_name":"Paz, José C.","first_name":"José C."},{"last_name":"Mirmira","full_name":"Mirmira, Raghavendra G.","first_name":"Raghavendra G."},{"first_name":"Antonia","full_name":"Gutiérrez, Antonia","last_name":"Gutiérrez"},{"first_name":"Francisco J.","last_name":"Alonso","full_name":"Alonso, Francisco J."},{"first_name":"Juan A.","last_name":"Segura","full_name":"Segura, Juan A."},{"first_name":"José M.","last_name":"Matés","full_name":"Matés, José M."},{"first_name":"Gert","last_name":"Lubec","full_name":"Lubec, Gert"},{"full_name":"Márquez, Javier","last_name":"Márquez","first_name":"Javier"}],"article_processing_charge":"No","external_id":{"pmid":["32042057"],"isi":["000560694800012"]},"title":"Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation","publisher":"Springer Nature","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"10","publication":"Scientific reports","date_published":"2020-02-10T00:00:00Z","doi":"10.1038/s41598-020-58264-4","date_created":"2020-02-16T23:00:49Z","_id":"7487","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-18T06:35:13Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"CaBe"}],"abstract":[{"text":"Glutaminase (GA) catalyzes the first step in mitochondrial glutaminolysis playing a key role in cancer metabolic reprogramming. Humans express two types of GA isoforms: GLS and GLS2. GLS isozymes have been consistently related to cell proliferation, but the role of GLS2 in cancer remains poorly understood. GLS2 is repressed in many tumor cells and a better understanding of its function in tumorigenesis may further the development of new therapeutic approaches. We analyzed GLS2 expression in HCC, GBM and neuroblastoma cells, as well as in monkey COS-7 cells. We studied GLS2 expression after induction of differentiation with phorbol ester (PMA) and transduction with the full-length cDNA of GLS2. In parallel, we investigated cell cycle progression and levels of p53, p21 and c-Myc proteins. Using the baculovirus system, human GLS2 protein was overexpressed, purified and analyzed for posttranslational modifications employing a proteomics LC-MS/MS platform. We have demonstrated a dual targeting of GLS2 in human cancer cells. Immunocytochemistry and subcellular fractionation gave consistent results demonstrating nuclear and mitochondrial locations, with the latter being predominant. Nuclear targeting was confirmed in cancer cells overexpressing c-Myc- and GFP-tagged GLS2 proteins. We assessed the subnuclear location finding a widespread distribution of GLS2 in the nucleoplasm without clear overlapping with specific nuclear substructures. GLS2 expression and nuclear accrual notably increased by treatment of SH-SY5Y cells with PMA and it correlated with cell cycle arrest at G2/M, upregulation of tumor suppressor p53 and p21 protein. A similar response was obtained by overexpression of GLS2 in T98G glioma cells, including downregulation of oncogene c-Myc. Furthermore, human GLS2 was identified as being hypusinated by MS analysis, a posttranslational modification which may be relevant for its nuclear targeting and/or function. Our studies provide evidence for a tumor suppressor role of GLS2 in certain types of cancer. The data imply that GLS2 can be regarded as a highly mobile and multilocalizing protein translocated to both mitochondria and nuclei. Upregulation of GLS2 in cancer cells induced an antiproliferative response with cell cycle arrest at the G2/M phase.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 10","publication_identifier":{"eissn":["20452322"]},"publication_status":"published","file":[{"file_id":"7495","checksum":"c780bd87476a9c9e12668ff66de3dc96","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-02-18T07:43:21Z","file_name":"2020_ScientificReport_Lopez.pdf","date_updated":"2020-07-14T12:47:59Z","file_size":4703751,"creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"1","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-020-80651-0"}]},"volume":10},{"abstract":[{"text":"The posterior parietal cortex (PPC) and frontal motor areas comprise a cortical network supporting goal-directed behaviour, with functions including sensorimotor transformations and decision making. In primates, this network links performed and observed actions via mirror neurons, which fire both when individuals perform an action and when they observe the same action performed by a conspecific. Mirror neurons are believed to be important for social learning, but it is not known whether mirror-like neurons occur in similar networks in other social species, such as rodents, or if they can be measured in such models using paradigms where observers passively view a demonstrator. Therefore, we imaged Ca2+ responses in PPC and secondary motor cortex (M2) while mice performed and observed pellet-reaching and wheel-running tasks, and found that cell populations in both areas robustly encoded several naturalistic behaviours. However, neural responses to the same set of observed actions were absent, although we verified that observer mice were attentive to performers and that PPC neurons responded reliably to visual cues. Statistical modelling also indicated that executed actions outperformed observed actions in predicting neural responses. These results raise the possibility that sensorimotor action recognition in rodents could take place outside of the parieto-frontal circuit, and underscore that detecting socially-driven neural coding depends critically on the species and behavioural paradigm used.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"03","publication_status":"published","publication_identifier":{"eissn":["20452322"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2020_ScientificReports_Tombaz.pdf","date_created":"2020-04-06T10:44:23Z","creator":"dernst","file_size":2621249,"date_updated":"2020-07-14T12:48:01Z","file_id":"7644","checksum":"e6cfaaaf7986532132934400038b824a","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"issue":"1","volume":10,"_id":"7632","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-18T10:25:13Z","ddc":["570"],"department":[{"_id":"SaSi"}],"file_date_updated":"2020-07-14T12:48:01Z","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2020","isi":1,"has_accepted_license":"1","publication":"Scientific reports","day":"27","date_created":"2020-04-05T22:00:47Z","doi":"10.1038/s41598-020-62089-6","date_published":"2020-03-27T00:00:00Z","article_number":"5559","citation":{"ista":"Tombaz T, Dunn BA, Hovde K, Cubero RJ, Mimica B, Mamidanna P, Roudi Y, Whitlock JR. 2020. Action representation in the mouse parieto-frontal network. Scientific reports. 10(1), 5559.","chicago":"Tombaz, Tuce, Benjamin A. Dunn, Karoline Hovde, Ryan J Cubero, Bartul Mimica, Pranav Mamidanna, Yasser Roudi, and Jonathan R. Whitlock. “Action Representation in the Mouse Parieto-Frontal Network.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-62089-6.","ama":"Tombaz T, Dunn BA, Hovde K, et al. Action representation in the mouse parieto-frontal network. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-62089-6","apa":"Tombaz, T., Dunn, B. A., Hovde, K., Cubero, R. J., Mimica, B., Mamidanna, P., … Whitlock, J. R. (2020). Action representation in the mouse parieto-frontal network. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-62089-6","short":"T. Tombaz, B.A. Dunn, K. Hovde, R.J. Cubero, B. Mimica, P. Mamidanna, Y. Roudi, J.R. Whitlock, Scientific Reports 10 (2020).","ieee":"T. Tombaz et al., “Action representation in the mouse parieto-frontal network,” Scientific reports, vol. 10, no. 1. Springer Nature, 2020.","mla":"Tombaz, Tuce, et al. “Action Representation in the Mouse Parieto-Frontal Network.” Scientific Reports, vol. 10, no. 1, 5559, Springer Nature, 2020, doi:10.1038/s41598-020-62089-6."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000560406800007"]},"article_processing_charge":"No","author":[{"last_name":"Tombaz","full_name":"Tombaz, Tuce","first_name":"Tuce"},{"last_name":"Dunn","full_name":"Dunn, Benjamin A.","first_name":"Benjamin A."},{"first_name":"Karoline","full_name":"Hovde, Karoline","last_name":"Hovde"},{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","first_name":"Ryan J","full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867","last_name":"Cubero"},{"full_name":"Mimica, Bartul","last_name":"Mimica","first_name":"Bartul"},{"last_name":"Mamidanna","full_name":"Mamidanna, Pranav","first_name":"Pranav"},{"first_name":"Yasser","last_name":"Roudi","full_name":"Roudi, Yasser"},{"first_name":"Jonathan R.","full_name":"Whitlock, Jonathan R.","last_name":"Whitlock"}],"title":"Action representation in the mouse parieto-frontal network"},{"department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:48:05Z","ddc":["570"],"date_updated":"2023-08-21T07:00:17Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"7931","volume":10,"language":[{"iso":"eng"}],"file":[{"file_id":"7947","checksum":"099e51611a5b7ca04244d03b2faddf33","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_ScientificReports_Uroshlev.pdf","date_created":"2020-06-08T06:27:32Z","creator":"dernst","file_size":1001724,"date_updated":"2020-07-14T12:48:05Z"}],"publication_status":"published","publication_identifier":{"eissn":["20452322"]},"intvolume":" 10","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data."}],"title":"A method for identification of the methylation level of CpG islands from NGS data","article_processing_charge":"No","external_id":{"isi":["000560774200007"]},"author":[{"first_name":"Leonid A.","full_name":"Uroshlev, Leonid A.","last_name":"Uroshlev"},{"first_name":"Eldar T.","last_name":"Abdullaev","full_name":"Abdullaev, Eldar T."},{"last_name":"Umarova","full_name":"Umarova, Iren R.","first_name":"Iren R."},{"first_name":"Irina A.","last_name":"Il’Icheva","full_name":"Il’Icheva, Irina A."},{"first_name":"Larisa A.","last_name":"Panchenko","full_name":"Panchenko, Larisa A."},{"first_name":"Robert V.","last_name":"Polozov","full_name":"Polozov, Robert V."},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nechipurenko, Yury D.","last_name":"Nechipurenko","first_name":"Yury D."},{"full_name":"Grokhovsky, Sergei L.","last_name":"Grokhovsky","first_name":"Sergei L."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-65406-1","ama":"Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 2020;10. doi:10.1038/s41598-020-65406-1","ieee":"L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer Nature, 2020.","short":"L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020).","mla":"Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635, Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.","ista":"Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635.","chicago":"Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-65406-1."},"article_number":"8635","date_created":"2020-06-07T22:00:51Z","doi":"10.1038/s41598-020-65406-1","date_published":"2020-05-25T00:00:00Z","publication":"Scientific Reports","day":"25","year":"2020","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"citation":{"apa":"Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-72848-0","ama":"Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10. doi:10.1038/s41598-020-72848-0","ieee":"A. Deichler et al., “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” Scientific Reports, vol. 10. Springer Nature, 2020.","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","mla":"Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol. 10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0.","ista":"Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220.","chicago":"Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Deichler","full_name":"Deichler, Alfonso","first_name":"Alfonso"},{"last_name":"Carrasco","full_name":"Carrasco, Denisse","first_name":"Denisse"},{"first_name":"Luciana","last_name":"Lopez-Jury","full_name":"Lopez-Jury, Luciana"},{"id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A","full_name":"Vega Zuniga, Tomas A","last_name":"Vega Zuniga"},{"first_name":"Natalia","last_name":"Marquez","full_name":"Marquez, Natalia"},{"first_name":"Jorge","full_name":"Mpodozis, Jorge","last_name":"Mpodozis"},{"full_name":"Marin, Gonzalo","last_name":"Marin","first_name":"Gonzalo"}],"article_processing_charge":"No","external_id":{"isi":["000577142600032"]},"title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents","article_number":"16220","has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Scientific Reports","date_published":"2020-10-01T00:00:00Z","doi":"10.1038/s41598-020-72848-0","date_created":"2020-10-11T22:01:14Z","acknowledgement":"We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-08-22T09:58:21Z","ddc":["570"],"department":[{"_id":"MaJö"}],"file_date_updated":"2020-10-12T12:39:10Z","_id":"8643","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["20452322"]},"publication_status":"published","file":[{"file_id":"8651","checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-10-12T12:39:10Z","file_name":"2020_ScientificReport_Deichler.pdf","date_updated":"2020-10-12T12:39:10Z","file_size":3906744,"creator":"dernst"}],"language":[{"iso":"eng"}],"volume":10,"abstract":[{"text":"The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 10"},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Scientific Reports","day":"02","year":"2019","has_accepted_license":"1","isi":1,"date_created":"2019-09-15T22:00:42Z","doi":"10.1038/s41598-019-48930-7","date_published":"2019-09-02T00:00:00Z","article_number":"12625","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Fenu, M., Bettermann, T., Vogl, C., Darwish-Miranda, N., Schramel, J., Jenner, F., & Ribitsch, I. (2019). A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-48930-7","ama":"Fenu M, Bettermann T, Vogl C, et al. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-48930-7","ieee":"M. Fenu et al., “A novel magnet-based scratch method for standardisation of wound-healing assays,” Scientific Reports, vol. 9, no. 1. Springer Nature, 2019.","short":"M. Fenu, T. Bettermann, C. Vogl, N. Darwish-Miranda, J. Schramel, F. Jenner, I. Ribitsch, Scientific Reports 9 (2019).","mla":"Fenu, M., et al. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports, vol. 9, no. 1, 12625, Springer Nature, 2019, doi:10.1038/s41598-019-48930-7.","ista":"Fenu M, Bettermann T, Vogl C, Darwish-Miranda N, Schramel J, Jenner F, Ribitsch I. 2019. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 9(1), 12625.","chicago":"Fenu, M., T. Bettermann, C. Vogl, Nasser Darwish-Miranda, J. Schramel, F. Jenner, and I. Ribitsch. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-48930-7."},"title":"A novel magnet-based scratch method for standardisation of wound-healing assays","article_processing_charge":"No","external_id":{"isi":["000483697800007"],"pmid":["31477739"]},"author":[{"last_name":"Fenu","full_name":"Fenu, M.","first_name":"M."},{"first_name":"T.","full_name":"Bettermann, T.","last_name":"Bettermann"},{"first_name":"C.","last_name":"Vogl","full_name":"Vogl, C."},{"first_name":"Nasser","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8821-8236","full_name":"Darwish-Miranda, Nasser","last_name":"Darwish-Miranda"},{"first_name":"J.","full_name":"Schramel, J.","last_name":"Schramel"},{"first_name":"F.","full_name":"Jenner, F.","last_name":"Jenner"},{"first_name":"I.","full_name":"Ribitsch, I.","last_name":"Ribitsch"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"A novel magnetic scratch method achieves repeatability, reproducibility and geometric control greater than pipette scratch assays and closely approximating the precision of cell exclusion assays while inducing the cell injury inherently necessary for wound healing assays. The magnetic scratch is affordable, easily implemented and standardisable and thus may contribute toward better comparability of data generated in different studies and laboratories."}],"intvolume":" 9","month":"09","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2019_ScientificReports_Fenu.pdf","date_created":"2019-09-16T12:42:40Z","creator":"dernst","file_size":3523795,"date_updated":"2020-07-14T12:47:42Z","checksum":"9cfd986d4108e288cc72276ef047ab0c","file_id":"6879","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["20452322"]},"issue":"1","volume":9,"_id":"6867","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2023-08-29T07:55:15Z","file_date_updated":"2020-07-14T12:47:42Z","department":[{"_id":"Bio"}]}]