---
_id: '12706'
abstract:
- lang: eng
  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.
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."
article_processing_charge: No
article_type: original
author:
- first_name: Jody C.
  full_name: Mckerral, Jody C.
  last_name: Mckerral
- first_name: Maria
  full_name: Kleshnina, Maria
  id: 4E21749C-F248-11E8-B48F-1D18A9856A87
  last_name: Kleshnina
- first_name: Vladimir
  full_name: Ejov, Vladimir
  last_name: Ejov
- first_name: Louise
  full_name: Bartle, Louise
  last_name: Bartle
- first_name: James G.
  full_name: Mitchell, James G.
  last_name: Mitchell
- first_name: Jerzy A.
  full_name: Filar, Jerzy A.
  last_name: Filar
citation:
  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>
  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>.
  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.
  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.
  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>.
  short: J.C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J.G. Mitchell, J.A. Filar,
    PLoS One 18 (2023) e0279838.
date_created: 2023-03-05T23:01:05Z
date_published: 2023-02-27T00:00:00Z
date_updated: 2023-10-17T12:53:30Z
day: '27'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0279838
external_id:
  isi:
  - '000996122900022'
  pmid:
  - '36848357'
file:
- access_level: open_access
  checksum: 798ed5739a4117b03173e5d56e0534c9
  content_type: application/pdf
  creator: cchlebak
  date_created: 2023-03-07T10:26:45Z
  date_updated: 2023-03-07T10:26:45Z
  file_id: '12712'
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  file_size: 1257003
  relation: main_file
  success: 1
file_date_updated: 2023-03-07T10:26:45Z
has_accepted_license: '1'
intvolume: '        18'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: e0279838
pmid: 1
publication: PLoS One
publication_identifier:
  eissn:
  - 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur
  equations
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2023'
...
---
_id: '12758'
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.
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.
article_number: e0282689
article_processing_charge: No
article_type: original
author:
- first_name: Marina A.
  full_name: Pak, Marina A.
  last_name: Pak
- first_name: Karina A.
  full_name: Markhieva, Karina A.
  last_name: Markhieva
- first_name: Mariia S.
  full_name: Novikova, Mariia S.
  last_name: Novikova
- first_name: Dmitry S.
  full_name: Petrov, Dmitry S.
  last_name: Petrov
- first_name: Ilya S.
  full_name: Vorobyev, Ilya S.
  last_name: Vorobyev
- first_name: Ekaterina
  full_name: Maksimova, Ekaterina
  id: 2FBE0DE4-F248-11E8-B48F-1D18A9856A87
  last_name: Maksimova
- first_name: Fyodor
  full_name: Kondrashov, Fyodor
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
- first_name: Dmitry N.
  full_name: Ivankov, Dmitry N.
  last_name: Ivankov
citation:
  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>
  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>.
  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.
  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.
  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>.
  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).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-16T00:00:00Z
date_updated: 2023-08-01T13:47:14Z
day: '16'
ddc:
- '570'
department:
- _id: FyKo
- _id: MaRo
doi: 10.1371/journal.pone.0282689
external_id:
  isi:
  - '000985134400106'
file:
- access_level: open_access
  checksum: 0281bdfccf8d76c4e08dd011c603f6b6
  content_type: application/pdf
  creator: dernst
  date_created: 2023-03-27T07:09:08Z
  date_updated: 2023-03-27T07:09:08Z
  file_id: '12771'
  file_name: 2023_PLoSOne_Pak.pdf
  file_size: 856625
  relation: main_file
  success: 1
file_date_updated: 2023-03-27T07:09:08Z
has_accepted_license: '1'
intvolume: '        18'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS ONE
publication_identifier:
  eissn:
  - 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using AlphaFold to predict the impact of single mutations on protein stability
  and function
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2023'
...
---
_id: '12759'
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.
acknowledged_ssus:
- _id: EM-Fac
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)."
article_number: e0277148
article_processing_charge: No
article_type: original
author:
- first_name: Jason Seth
  full_name: Rothman, Jason Seth
  last_name: Rothman
- first_name: Carolina
  full_name: Borges Merjane, Carolina
  id: 4305C450-F248-11E8-B48F-1D18A9856A87
  last_name: Borges Merjane
  orcid: 0000-0003-0005-401X
- first_name: Noemi
  full_name: Holderith, Noemi
  last_name: Holderith
- first_name: Peter M
  full_name: Jonas, Peter M
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
- first_name: R.
  full_name: Angus Silver, R.
  last_name: Angus Silver
citation:
  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>
  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>
  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>.
  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.
  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.
  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>.
  short: J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver,
    PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-08-01T13:46:39Z
day: '17'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1371/journal.pone.0277148
ec_funded: 1
external_id:
  isi:
  - '001024737400001'
file:
- access_level: open_access
  checksum: 2380331ec27cc87808826fc64419ac1c
  content_type: application/pdf
  creator: dernst
  date_created: 2023-03-27T06:51:09Z
  date_updated: 2023-03-27T06:51:09Z
  file_id: '12770'
  file_name: 2023_PLoSOne_Rothman.pdf
  file_size: 7290413
  relation: main_file
  success: 1
file_date_updated: 2023-03-27T06:51:09Z
has_accepted_license: '1'
intvolume: '        18'
isi: 1
issue: 3 March
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '692692'
  name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z00312
  name: The Wittgenstein Prize
- _id: 2696E7FE-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: V00739
  name: Structural plasticity at mossy fiber-CA3 synapses
publication: PLoS ONE
publication_identifier:
  eissn:
  - 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Validation of a stereological method for estimating particle size and density
  from 2D projections with high accuracy
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2023'
...
---
_id: '11704'
abstract:
- lang: eng
  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.
article_number: e0269975
article_processing_charge: No
article_type: original
author:
- first_name: Nazmi B
  full_name: Budanur, Nazmi B
  id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
  last_name: Budanur
  orcid: 0000-0003-0423-5010
- first_name: Björn
  full_name: Hof, Björn
  id: 3A374330-F248-11E8-B48F-1D18A9856A87
  last_name: Hof
  orcid: 0000-0003-2057-2754
citation:
  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>
  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>.
  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.
  ista: Budanur NB, Hof B. 2022. An autonomous compartmental model for accelerating
    epidemics. PLoS ONE. 17(7), e0269975.
  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>.
  short: N.B. Budanur, B. Hof, PLoS ONE 17 (2022).
date_created: 2022-07-31T22:01:48Z
date_published: 2022-07-18T00:00:00Z
date_updated: 2023-08-03T12:24:22Z
day: '18'
ddc:
- '510'
department:
- _id: BjHo
doi: 10.1371/journal.pone.0269975
external_id:
  isi:
  - '000911392100055'
file:
- access_level: open_access
  checksum: 1ddd9b91e6dec31ab0e7a8433ca2d452
  content_type: application/pdf
  creator: dernst
  date_created: 2022-08-01T08:02:38Z
  date_updated: 2022-08-01T08:02:38Z
  file_id: '11712'
  file_name: 2022_PLoSONE_Budanur.pdf
  file_size: 1421256
  relation: main_file
  success: 1
file_date_updated: 2022-08-01T08:02:38Z
has_accepted_license: '1'
intvolume: '        17'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS ONE
publication_identifier:
  eissn:
  - 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
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  - id: '11711'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: An autonomous compartmental model for accelerating epidemics
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2022'
...
---
_id: '9816'
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."
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.
article_number: e0255267
article_processing_charge: Yes
article_type: original
author:
- first_name: Michal
  full_name: Hledik, Michal
  id: 4171253A-F248-11E8-B48F-1D18A9856A87
  last_name: Hledik
- first_name: Jitka
  full_name: Polechova, Jitka
  id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
  last_name: Polechova
  orcid: 0000-0003-0951-3112
- first_name: Mathias
  full_name: Beiglböck, Mathias
  last_name: Beiglböck
- first_name: Anna Nele
  full_name: Herdina, Anna Nele
  last_name: Herdina
- first_name: Robert
  full_name: Strassl, Robert
  last_name: Strassl
- first_name: Martin
  full_name: Posch, Martin
  last_name: Posch
citation:
  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>
  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>.
  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.
  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.
  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>.
  short: M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch,
    PLoS ONE 16 (2021).
date_created: 2021-08-08T22:01:26Z
date_published: 2021-07-29T00:00:00Z
date_updated: 2023-08-10T14:26:32Z
day: '29'
ddc:
- '610'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0255267
external_id:
  isi:
  - '000685248200095'
  pmid:
  - '34324553'
file:
- access_level: open_access
  checksum: ae4df60eb62f4491278588548d0c1f93
  content_type: application/pdf
  creator: asandaue
  date_created: 2021-08-09T11:52:14Z
  date_updated: 2021-08-09T11:52:14Z
  file_id: '9835'
  file_name: 2021_PLoSONE_Hledík.pdf
  file_size: 773921
  relation: main_file
  success: 1
file_date_updated: 2021-08-09T11:52:14Z
has_accepted_license: '1'
intvolume: '        16'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
  eissn:
  - 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing
  program
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2021'
...
