Peer Review #3 of "Evaluation of outbreak response immunization in the control of pertussis using agent-based modeling (v0.1)"
Bibliographic record
Abstract
Background.Pertussis control remains a challenge due to recently observed effects of waning immunity to acellular vaccine and suboptimal vaccine coverage.Multiple outbreaks have been reported in different ages worldwide.For certain outbreaks, public health authorities can launch an outbreak response immunization campaign to control pertussis spread.We investigated effects of an outbreak response immunization targeting young adolescents in averting pertussis cases.Methods.We developed an agent-based model for pertussis transmission representing disease mechanism, waning immunity, vaccination schedule and pathogen transmission in a spatially-explicit 500,000-person contact network representing a typical Canadian Public Health district.Parameters were derived from literature and calibration.We used published cumulative incidence and dose-specific vaccine coverage to calibrate the model's epidemiological curves.We endogenized outbreak response by defining thresholds to trigger simulated immunization campaigns in the 10-14 age group offering 80% coverage.We ran paired simulations with and without outbreak response immunization and included those resulting in a single ORI within a 10year span.We calculated the number of cases averted attributable to outbreak immunization campaign in all ages, in the 10-14 age group and in infants.The count of cases averted were tested using Mann-Whitney U test to determine statistical significance.Numbers needed to vaccinate during immunization campaign to prevent a single case in respective age groups were derived from the model.We varied adult vaccine coverage, waning immunity parameters, immunization campaign eligibility and tested stronger vaccination boosting effect in sensitivity analyses.Results.189 qualified paired-runs were analyzed.On average, ORI was triggered every 26 years.On a per-run basis, there were an average of 124, 243 and 429 pertussis cases averted across all age groups within 1, 3 and 10 years of a campaign, respectively.During the same time periods, 53, 96, and 163 cases were averted in the 10-14 age group, and 6, 11, 20 in infants under 1 (p<0.001,all groups).Numbers needed to vaccinate ranged from 49 to 221, from 130 to 519 and from PeerJ reviewing PDF | (2016:02:9057:2:0:NEW
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot 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.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.015 | 0.122 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.133 | 0.033 |
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.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
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".