Additional file 1 of Cellular transcriptional alterations of peripheral blood in Alzheimer’s disease
Bibliographic record
Abstract
Additional file 1: Figure S1. Comparison of the NLR between MCI and NC in different datasets using different computational methods. NLR, neutrophil-to-lymphocyte ratio. Figure S2. Correlation between immune cell proportion and cognition measurements in AD and NC individuals. Correlations were assessed using Pearson’s correlation test. MoCA-B, Montreal Cognitive Assessment Basic; MMSE, Mini-Mental State Examination. Figure S3. Correlation between immune cell proportion and cognition measurements in all (i.e., AD, MCI, and NC) individuals. Figure S4. Demographic characteristics of participants across datasets. (A) The number of individuals for each diagnosis in each dataset. (B) Age distribution of participants across diagnosis groups in each dataset. The comparison was assessed with the Wilcoxon test. (C) Gender composition of subjects across each group of each dataset. The comparison was assessed with the Fisher test. Figure S5. Overlap of differentially expressed genes (DEG) in AD patients identified with limma (red) and the Wilcoxon test (blue). P-values for hypergeometric tests of pairwise overlaps are shown at the top. Figure S6. Bulk DEGs in MCI compared with NC. (A) Venn diagram shows the overlap of bulk DEGs in MCI across four blood transcriptomic datasets. (B-C) The top enriched biological processes of up (B) and down (C) regulated genes in MCI compared with NC in each dataset. The point size represents the number of DE genes in the corresponding pathway. Color represents the significant level (i.e., FDR). Figure S7. Overlap between bulk DEGs (blue) and DEGs in each cell type (red) of AD. P values for hypergeometric tests of pairwise overlaps are shown at the top. Figure S8. Top ten hub genes with high degree centrality or clustering coefficients in Modules 2 and 3. Figure S9. Spearman correlation between expression levels DEGs of AD neutrophils and MRI biomarkers for AD diagnosis and progression, where only genes with significant association with at least one MRI feature were shown. Figure S10. Top enriched biological processes of down (A) and up (B) regulated genes in AD compared with NC. Figure S11. Correlation between the neutrophil abundance score and Braak tau neurofibrillary tangle staging score in the cerebellum. The association was assessed using the Pearson correlation test. Figure S12. Comparison of immune cell proportion in the cerebellum (A) and temporal cortex (B) between AD and NC. Figure S13. Overlap of cell-intrict DEGs among different dataset. Blue: our study; Red: Kuan et. al’s study; Yellow: Kuan et. al’s study.
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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 | 0.002 | 0.023 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.762 | 0.114 |
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".