Comparison of Microbiota in the Upper Versus Lower Respiratory Tract in Children During Health and Respiratory Disease: a Protocol for a Systematic Review
Bibliographic record
Abstract
Abstract Background: Several species of organisms reside in the upper airways of healthy infants and children. In most cases they do no harm to the host despite being potentially pathogenic. In contrast, the lung in healthy people was considered to be a sterile environment, but sophisticated techniques have recently demonstrated colonization by a complex population of microorganisms in healthy adults. It is unclear if a similar situation happens in healthy children. In children with respiratory disease, several micro-organisms can be recovered from the upper as well as lower respiratory tracts. However, the correlation between organisms recovered from the two sites is unclear. This systematic review is designed to explore the microbial composition of the respiratory system in apparently healthy asymptomatic children, comparing the organisms identified in the upper airways versus the lungs. We also intend to compare the site-specific prevalence and pattern of organisms in healthy children versus those with various respiratory diseases. We will also compare the organism identified in the upper airway versus the lungs in children with respiratory disease.Methods: We will search the following electronic databases: Medline, Embase and the Cochrane Library. Reference list of relevant studies will be examined for links to potential related articles. Two reviewers will independently determine study eligibility. The methodological quality of the observational included studies will be scored using the Newcastle Ottawa Scale tool for assessing risk of bias. We will extract data from included studies and perform meta-analysis where feasible.Results: The search strategy will be refined and the literature search will take place independently by two authors. Final stage will include analyses and writing.Discussion: Through the publication of this protocol, readers will be able to assess the research question and methods presented in this protocol. Upon publication of the review, readers will be able to assess whether the review was conducted according to pre-defined plan. Researchers will be aware that the review is underway, thereby avoid duplication, and be able to use it as a basis for planning similar reviews.PROSPERO registration number: CRD42020202115
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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 | 0.079 | 0.099 |
| Meta-epidemiology (narrow) | 0.006 | 0.005 |
| Meta-epidemiology (broad) | 0.022 | 0.020 |
| Bibliometrics | 0.016 | 0.014 |
| Science and technology studies | 0.004 | 0.005 |
| Scholarly communication | 0.007 | 0.009 |
| Open science | 0.006 | 0.005 |
| Research integrity | 0.009 | 0.006 |
| Insufficient payload (model declined to judge) | 0.044 | 0.007 |
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".