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Record W2914582688 · doi:10.1093/cid/ciz115

Reply to Skowronski, De Serres, and Orenstein

2019· letter· en· W2914582688 on OpenAlexaff
Mark G. Thompson, Michael L. Jackson, Annette K. Regan, Mark A. Katz, Jeffrey C. Kwong, Sarah Ball, Kimberley Simmonds, Nicola P. Klein, Allison L. Naleway

Bibliographic record

VenueClinical Infectious Diseases · 2019
Typeletter
Languageen
FieldMedicine
TopicInfluenza Virus Research Studies
Canadian institutionsUniversity of CalgaryInstitute for Clinical Evaluative Sciences
FundersCenters for Disease Control and Prevention
KeywordsMedicine

Abstract

fetched live from OpenAlex

To the Editor—We agree with Skowronski et al [1] that caution is required in conducting and interpreting studies of influenza vaccine effectiveness (IVE) using medical and public health data. Indeed, in our stratified results and discussion, we addressed many of the points the authors raised regarding IVE differences between sites, by illness severity (and thus thresholds for admission), and during peak and nonpeak weeks of influenza circulation [2]. We agree that clinician-ordered testing may bias IVE results if selection of who is tested is associated with both the risk of influenza positivity and the probability of influenza vaccination. Obviously, in the PREVENT cohort, clinicians often tested women with suspected influenza virus infection, and thus influenza positivity was high. Therefore, the risk of bias depends on the association between testing and the probability of vaccination. As we described in our article, published findings regarding this association are mixed. In a simulation study of the possible impact of selection bias on IVE estimates using the test-negative design (TND), Jackson et al found that bias from differential care seeking by patients was only meaningful (ie, reduced a true IVE of 50% by >5%) when vaccination doubled the likelihood of care seeking [3]. If we apply the same model but substitute clinician testing for patient care seeking as the action that selects patients into a study, Jackson et al’s simulation suggests that clinician testing among vaccinated versus unvaccinated pregnant women would have to differ by >2-fold in order to meaningfully bias IVE estimates. We acknowledge that the description of vaccination documentation in our article was limited, and greater detail on these methods is now published [4]. Most prospective IVE networks rely in part or entirely on self-reported vaccination status, which can increase false positive reports and thus reduce specificity of vaccine exposure measurement. In contrast, our study exclusively used vaccination documentation from medical records and registries, which can increase false negative records and thus reduce sensitivity. In a recent simulation study, Jackson et al concluded that low sensitivity presented a lesser risk of bias to IVE estimates using TND than did low specificity; records with only 40% sensitivity to true vaccination status could result in an IVE estimate of 40% when the true IVE is 50% [5]. This is consistent with our interpretation that we likely underestimated true IVE. Finally, we are concerned that a reader might misinterpret Skowronski et al’s observation that we focused on “general laboratory-submissions without standardization of the influenza testing-indication” to mean that we simply sampled all patients with clinical testing. Our study focused on real-time reverse transcription polymerase chain reaction testing among pregnant women hospitalized during weeks of local influenza circulation with a diagnosis associated with influenza in previous studies. Although prospective IVE networks play a vital role in IVE monitoring, further population-based research like PREVENT that builds on our methodological strengths and mitigates limitations is also needed to assess IVE in preventing less frequent and severe outcomes, such as influenza illness that is a primary or secondary cause of hospitalization during pregnancy. Financial support. This study was funded in part by the US Centers for Disease Control and Prevention. Potential conflicts of interest. A. N. reports grants from Pfizer, MedImmune/AstraZeneca, and Merck, outside the submitted work. N. K. reports grants from GlaxoSmithKline, Sanofi Pasteur, Pfizer, Protein Science, Merck & Co, MedImmune, Novartis (now GlaxoSmithKline), and Dynavax, outside the submitted work. All other authors report no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.006
metaresearch head score (Gemma)0.034
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: Not applicable
GenreCandidate signal: Commentary · Consensus signal: Commentary
Teacher disagreement score0.058
Threshold uncertainty score0.033

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0060.034
Meta-epidemiology (narrow)0.0010.001
Meta-epidemiology (broad)0.0020.001
Bibliometrics0.0010.001
Science and technology studies0.0040.003
Scholarly communication0.0040.004
Open science0.0020.002
Research integrity0.0580.035
Insufficient payload (model declined to judge)0.0070.006

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.099
GPT teacher head0.443
Teacher spread0.345 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designNot applicable
Domainnot available
GenreCommentary

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations2
Published2019
Admission routes1
Has abstractno

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