Additional file 2 of The Parkinson’s disease risk gene cathepsin B promotes fibrillar alpha-synuclein clearance, lysosomal function and glucocerebrosidase activity in dopaminergic neurons
Bibliographic record
Abstract
Supplementary Material 2. Supplemental Figure 1: A) Immunofluorescent staining of parental (AIW002-02) and SNCA-KO iPSCs for pluripotency markers. B) Karyotype analysis of SNCA-KO iPSCs. C) Genome stability analysis of SNCA-KO iPSCs. D) Protein levels of alpha-synuclein in control versus SNCA-KO iPSCs after differentiation into dopaminergic neurons. E) Pluripotency marker expression in CTSB-KO iPSCs. F) Karyotype analysis of CTSB-KO iPSCs. G) Genome stability analysis of CTSB-KO iPSCs. H) Protein levels of cathepsin B in control versus CTSB-KO iPSCs after differentiation into dopaminergic neurons. Supplemental Figure 2:A) Differentiation of AIW002-2 iPSCs into dopaminergic neurons labelled for Map2 and tyrosine hydroxylase (TH). B) Percentage of TH-positive cells at 2 , 4, 6 and 8 weeks of differentiation. C) Representative electron microscopy imaging of a-syn PFFs. D) Measurement of a-syn PFF fibril size. Supplementary Figure 3: Immunofluorescent characterization of 5-month old midbrain organoids generated from SNCA triplication or SNCA-KO iPSCs. A-C) Markers of specific cell types present in SNCA triplication midbrain organoids including dopaminergic neurons (panel A, TH and GIRK2), inhibitory neurons (panel B, Map2 and GAD67), and astrocytes (panel C, GFAP). Oligodendrocytes (OLIG2) were not detected. D, E) Representative immunofluorescent images depicting a-syn expression in either SNCA triplication or SNCA-KO organoids demonstrating specificity of a-syn detection. Nuclei are indicated in blue (Hoechst), total neuronal content indicated in yellow (Map2), dopaminergic neurons are stained in red (TH – tyrosine hydroxylase), and a-syn is shown in green.
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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 | 0.001 | 0.016 |
| Meta-epidemiology (narrow) | 0.001 | 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) | 0.871 | 0.164 |
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".