Additional file 1 of Does in utero HIV exposure and the early nutritional environment influence infant development and immune outcomes? Findings from a pilot study in Pretoria, South Africa
Bibliographic record
Abstract
Additional file 1: Supplementary Figure S1. Sequential gating approach for the measurement of CCR2 expression by CD14+ monocytes. The sequential gating approached used was as follows: First, the viable (7-AAD negative; region ‘Viable”) cells were identified using a 7-AAD vs SS Log density plot. A “Viable” region was created around the 7-AAD negative cells. Gated on the “Viable”cells, a SSLog vs FS plot was used to capture intact cells in the “E” region. CD14+ monocytes were identified (“CD14+” region) using a CD14 vs SS Log density plot that were gated on viable, intact cells (“E” region). CD14+ monocytes that express CCR2 were quantified using a CD192 (CCR2) vs SS Log plot. The proportion of CD14+/CCR2+ cells were captured in the “CD14+ CCR2+” region. The gating strategy followed to quantify CCR2 expression by CD16+ neutrophils was similar to what was described for CD14+ monocytes, but instead of identifying CD14+ monocytes, CD16+ neutrophils were identified (“CD16+” region) using a CD16 vs SS Log density plot that were gated on viable, intact cells (“E” region). CD16+ neutrophils that express CCR2 were quantified using a CD192 (CCR2) vs SS Log plot. The proportion of CD14+/CCR2+ cells was captured in the “CD16+ CCR2+” region.
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 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 | 0.002 | 0.033 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.741 | 0.048 |
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".