[{"doi":"10.1371/journal.pone.0279838","article_processing_charge":"No","publisher":"Public Library of Science","date_updated":"2023-10-17T12:53:30Z","_id":"12706","type":"journal_article","page":"e0279838","ddc":["000"],"quality_controlled":"1","isi":1,"year":"2023","external_id":{"isi":["000996122900022"],"pmid":["36848357"]},"status":"public","publication":"PLoS One","pmid":1,"acknowledgement":"This research was supported by an Australian Government Research Training Program\r\n(RTP) Scholarship to JCM (https://www.dese.gov.au), and LB is supported by the Centre de\r\nrecherche sur le vieillissement Fellowship Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","date_published":"2023-02-27T00:00:00Z","author":[{"full_name":"Mckerral, Jody C.","last_name":"Mckerral","first_name":"Jody C."},{"last_name":"Kleshnina","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","full_name":"Kleshnina, Maria","first_name":"Maria"},{"first_name":"Vladimir","last_name":"Ejov","full_name":"Ejov, Vladimir"},{"full_name":"Bartle, Louise","last_name":"Bartle","first_name":"Louise"},{"last_name":"Mitchell","full_name":"Mitchell, James G.","first_name":"James G."},{"first_name":"Jerzy A.","full_name":"Filar, Jerzy A.","last_name":"Filar"}],"day":"27","scopus_import":"1","title":"Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations","oa_version":"Published Version","volume":18,"article_type":"original","date_created":"2023-03-05T23:01:05Z","has_accepted_license":"1","intvolume":"        18","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-MacArthur differential equations to eliminate prey-mass dependency, facilitating an in depth analytic study of the equations which incorporates scaling parameters’ contributions to coexistence. We define the functional response term to match empirical findings, and examine situations where metabolic theory derivations and observation diverge. The dynamical properties of the Rosenzweig-MacArthur system, encompassing the distribution of size-abundance equilibria, the scaling of period and amplitude of population cycling, and relationships between predator and prey abundances, are consistent with empirical observation. Our parameterisation is an accurate minimal model across 15+ orders of mass magnitude.","lang":"eng"}],"publication_identifier":{"eissn":["1932-6203"]},"publication_status":"published","file_date_updated":"2023-03-07T10:26:45Z","month":"02","department":[{"_id":"KrCh"}],"file":[{"date_updated":"2023-03-07T10:26:45Z","creator":"cchlebak","date_created":"2023-03-07T10:26:45Z","file_size":1257003,"file_id":"12712","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_PLOSOne_Mckerral.pdf","checksum":"798ed5739a4117b03173e5d56e0534c9","relation":"main_file"}],"oa":1,"language":[{"iso":"eng"}],"issue":"2","citation":{"ieee":"J. C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J. G. Mitchell, and J. A. Filar, “Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations,” <i>PLoS One</i>, vol. 18, no. 2. Public Library of Science, p. e0279838, 2023.","short":"J.C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J.G. Mitchell, J.A. Filar, PLoS One 18 (2023) e0279838.","ama":"Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. <i>PLoS One</i>. 2023;18(2):e0279838. doi:<a href=\"https://doi.org/10.1371/journal.pone.0279838\">10.1371/journal.pone.0279838</a>","apa":"Mckerral, J. C., Kleshnina, M., Ejov, V., Bartle, L., Mitchell, J. G., &#38; Filar, J. A. (2023). Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0279838\">https://doi.org/10.1371/journal.pone.0279838</a>","mla":"Mckerral, Jody C., et al. “Empirical Parameterisation and Dynamical Analysis of the Allometric Rosenzweig-MacArthur Equations.” <i>PLoS One</i>, vol. 18, no. 2, Public Library of Science, 2023, p. e0279838, doi:<a href=\"https://doi.org/10.1371/journal.pone.0279838\">10.1371/journal.pone.0279838</a>.","ista":"Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. 2023. Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. PLoS One. 18(2), e0279838.","chicago":"Mckerral, Jody C., Maria Kleshnina, Vladimir Ejov, Louise Bartle, James G. Mitchell, and Jerzy A. Filar. “Empirical Parameterisation and Dynamical Analysis of the Allometric Rosenzweig-MacArthur Equations.” <i>PLoS One</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0279838\">https://doi.org/10.1371/journal.pone.0279838</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_identifier":{"eissn":["1932-6203"]},"publication_status":"published","file_date_updated":"2023-03-27T07:09:08Z","abstract":[{"lang":"eng","text":"AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and <pLDDT> metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding."}],"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        18","has_accepted_license":"1","article_type":"original","date_created":"2023-03-26T22:01:07Z","volume":18,"oa_version":"Published Version","title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","author":[{"last_name":"Pak","full_name":"Pak, Marina A.","first_name":"Marina A."},{"last_name":"Markhieva","full_name":"Markhieva, Karina A.","first_name":"Karina A."},{"first_name":"Mariia S.","full_name":"Novikova, Mariia S.","last_name":"Novikova"},{"first_name":"Dmitry S.","full_name":"Petrov, Dmitry S.","last_name":"Petrov"},{"full_name":"Vorobyev, Ilya S.","last_name":"Vorobyev","first_name":"Ilya S."},{"first_name":"Ekaterina","last_name":"Maksimova","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87","full_name":"Maksimova, Ekaterina"},{"orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"full_name":"Ivankov, Dmitry N.","last_name":"Ivankov","first_name":"Dmitry N."}],"scopus_import":"1","day":"16","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","citation":{"mla":"Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” <i>PLoS ONE</i>, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pone.0282689\">10.1371/journal.pone.0282689</a>.","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0282689\">https://doi.org/10.1371/journal.pone.0282689</a>","chicago":"Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” <i>PLoS ONE</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0282689\">https://doi.org/10.1371/journal.pone.0282689</a>.","ista":"Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689.","short":"M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).","ieee":"M. A. Pak <i>et al.</i>, “Using AlphaFold to predict the impact of single mutations on protein stability and function,” <i>PLoS ONE</i>, vol. 18, no. 3. Public Library of Science, 2023.","ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. <i>PLoS ONE</i>. 2023;18(3). doi:<a href=\"https://doi.org/10.1371/journal.pone.0282689\">10.1371/journal.pone.0282689</a>"},"language":[{"iso":"eng"}],"oa":1,"article_number":"e0282689","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_PLoSOne_Pak.pdf","checksum":"0281bdfccf8d76c4e08dd011c603f6b6","relation":"main_file","date_updated":"2023-03-27T07:09:08Z","creator":"dernst","file_size":856625,"date_created":"2023-03-27T07:09:08Z","file_id":"12771"}],"department":[{"_id":"FyKo"},{"_id":"MaRo"}],"month":"03","quality_controlled":"1","ddc":["570"],"type":"journal_article","date_updated":"2023-08-01T13:47:14Z","_id":"12758","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0282689","article_processing_charge":"No","date_published":"2023-03-16T00:00:00Z","acknowledgement":"The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021.","publication":"PLoS ONE","status":"public","external_id":{"isi":["000985134400106"]},"year":"2023","isi":1},{"doi":"10.1371/journal.pone.0277148","article_processing_charge":"No","publisher":"Public Library of Science","date_updated":"2023-08-01T13:46:39Z","_id":"12759","type":"journal_article","ddc":["570"],"quality_controlled":"1","year":"2023","isi":1,"external_id":{"isi":["001024737400001"]},"project":[{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"V00739","name":"Structural plasticity at mossy fiber-CA3 synapses","_id":"2696E7FE-B435-11E9-9278-68D0E5697425"}],"publication":"PLoS ONE","status":"public","ec_funded":1,"acknowledgement":"We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157).","date_published":"2023-03-17T00:00:00Z","author":[{"full_name":"Rothman, Jason Seth","last_name":"Rothman","first_name":"Jason Seth"},{"orcid":"0000-0003-0005-401X","first_name":"Carolina","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","full_name":"Borges Merjane, Carolina"},{"last_name":"Holderith","full_name":"Holderith, Noemi","first_name":"Noemi"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"R.","last_name":"Angus Silver","full_name":"Angus Silver, R."}],"day":"17","scopus_import":"1","title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","oa_version":"Published Version","volume":18,"article_type":"original","date_created":"2023-03-26T22:01:07Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density."}],"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        18","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_status":"published","publication_identifier":{"eissn":["1932-6203"]},"file_date_updated":"2023-03-27T06:51:09Z","month":"03","department":[{"_id":"PeJo"}],"article_number":"e0277148","file":[{"file_id":"12770","creator":"dernst","date_updated":"2023-03-27T06:51:09Z","file_size":7290413,"date_created":"2023-03-27T06:51:09Z","checksum":"2380331ec27cc87808826fc64419ac1c","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2023_PLoSOne_Rothman.pdf","success":1}],"oa":1,"language":[{"iso":"eng"}],"issue":"3 March","citation":{"chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” <i>PLoS ONE</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0277148\">https://doi.org/10.1371/journal.pone.0277148</a>.","ista":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.","apa":"Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., &#38; Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0277148\">https://doi.org/10.1371/journal.pone.0277148</a>","mla":"Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” <i>PLoS ONE</i>, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pone.0277148\">10.1371/journal.pone.0277148</a>.","ama":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. <i>PLoS ONE</i>. 2023;18(3 March). doi:<a href=\"https://doi.org/10.1371/journal.pone.0277148\">10.1371/journal.pone.0277148</a>","ieee":"J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” <i>PLoS ONE</i>, vol. 18, no. 3 March. Public Library of Science, 2023.","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publication_identifier":{"eissn":["1932-6203"]},"publication_status":"published","file_date_updated":"2022-08-01T08:02:38Z","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"In Fall 2020, several European countries reported rapid increases in COVID-19 cases along with growing estimates of the effective reproduction rates. Such an acceleration in epidemic spread is usually attributed to time-dependent effects, e.g. human travel, seasonal behavioral changes, mutations of the pathogen etc. In this case however the acceleration occurred when counter measures such as testing and contact tracing exceeded their capacity limit. Considering Austria as an example, here we show that this dynamics can be captured by a time-independent, i.e. autonomous, compartmental model that incorporates these capacity limits. In this model, the epidemic acceleration coincides with the exhaustion of mitigation efforts, resulting in an increasing fraction of undetected cases that drive the effective reproduction rate progressively higher. We demonstrate that standard models which does not include this effect necessarily result in a systematic underestimation of the effective reproduction rate.","lang":"eng"}],"intvolume":"        17","has_accepted_license":"1","article_type":"original","date_created":"2022-07-31T22:01:48Z","volume":17,"title":"An autonomous compartmental model for accelerating epidemics","oa_version":"Published Version","author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010"},{"first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"scopus_import":"1","day":"18","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"7","citation":{"ieee":"N. B. Budanur and B. Hof, “An autonomous compartmental model for accelerating epidemics,” <i>PLoS ONE</i>, vol. 17, no. 7. Public Library of Science, 2022.","short":"N.B. Budanur, B. Hof, PLoS ONE 17 (2022).","ama":"Budanur NB, Hof B. An autonomous compartmental model for accelerating epidemics. <i>PLoS ONE</i>. 2022;17(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>","apa":"Budanur, N. B., &#38; Hof, B. (2022). An autonomous compartmental model for accelerating epidemics. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0269975\">https://doi.org/10.1371/journal.pone.0269975</a>","mla":"Budanur, Nazmi B., and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>, vol. 17, no. 7, e0269975, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>.","chicago":"Budanur, Nazmi B, and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pone.0269975\">https://doi.org/10.1371/journal.pone.0269975</a>.","ista":"Budanur NB, Hof B. 2022. An autonomous compartmental model for accelerating epidemics. PLoS ONE. 17(7), e0269975."},"language":[{"iso":"eng"}],"oa":1,"file":[{"date_updated":"2022-08-01T08:02:38Z","creator":"dernst","file_size":1421256,"date_created":"2022-08-01T08:02:38Z","file_id":"11712","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2022_PLoSONE_Budanur.pdf","checksum":"1ddd9b91e6dec31ab0e7a8433ca2d452","relation":"main_file"}],"article_number":"e0269975","department":[{"_id":"BjHo"}],"month":"07","quality_controlled":"1","ddc":["510"],"type":"journal_article","date_updated":"2023-08-03T12:24:22Z","_id":"11704","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0269975","article_processing_charge":"No","date_published":"2022-07-18T00:00:00Z","status":"public","publication":"PLoS ONE","external_id":{"isi":["000911392100055"]},"related_material":{"record":[{"id":"11711","status":"public","relation":"research_data"}]},"year":"2022","isi":1},{"volume":16,"article_type":"original","date_created":"2021-08-08T22:01:26Z","author":[{"first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"},{"last_name":"Polechova","full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka","orcid":"0000-0003-0951-3112"},{"full_name":"Beiglböck, Mathias","last_name":"Beiglböck","first_name":"Mathias"},{"full_name":"Herdina, Anna Nele","last_name":"Herdina","first_name":"Anna Nele"},{"last_name":"Strassl","full_name":"Strassl, Robert","first_name":"Robert"},{"first_name":"Martin","full_name":"Posch, Martin","last_name":"Posch"}],"scopus_import":"1","day":"29","oa_version":"Published Version","title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","publication_identifier":{"eissn":["1932-6203"]},"publication_status":"published","file_date_updated":"2021-08-09T11:52:14Z","has_accepted_license":"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        16","abstract":[{"lang":"eng","text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test."}],"department":[{"_id":"NiBa"}],"article_number":"e0255267","file":[{"creator":"asandaue","date_updated":"2021-08-09T11:52:14Z","file_size":773921,"date_created":"2021-08-09T11:52:14Z","file_id":"9835","content_type":"application/pdf","access_level":"open_access","file_name":"2021_PLoSONE_Hledík.pdf","success":1,"checksum":"ae4df60eb62f4491278588548d0c1f93","relation":"main_file"}],"month":"07","issue":"7","citation":{"mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <i>PLoS ONE</i>, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>.","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., &#38; Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>","chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>.","ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021).","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021.","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"date_updated":"2023-08-10T14:26:32Z","_id":"9816","type":"journal_article","doi":"10.1371/journal.pone.0255267","article_processing_charge":"Yes","publisher":"Public Library of Science","quality_controlled":"1","ddc":["610"],"year":"2021","isi":1,"external_id":{"pmid":["34324553"],"isi":["000685248200095"]},"pmid":1,"acknowledgement":"We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used.","date_published":"2021-07-29T00:00:00Z","publication":"PLoS ONE","status":"public"}]