Additional file 10 of A 3D human iPSC-derived multi-cell type neurosphere system to model cellular responses to chronic amyloidosis
Bibliographic record
Abstract
Supplementary Material 10: Figure S10: Neuronal gene expression changes during chronic amyloidosis in the presence of hiMG include APOE. A: Isolated neuronal cell populations from snRNA-seq on hiNSin ctrl, 3w and 5w Aβ conditions. Merged UMAPs of all 6 experimental groups displaying excitatory neuronsand inhibitory neurons. Note that the majority of 5w Aβ hiNSneurons cluster together in the individual neuronal populations. B: Quantification of total neuronal nuclei count in all 6 experimental groups. Note that only few neurons remain after chronic amyloidosis in the absence of hiMG. C: UMAP overlay of the three most significant DEGs APOE, SPP1 and FTL. Cell populations enriched with 5w Aβ hiNSneurons are encircled in dashed black lines. D: Heatmap depicting the top 15 most significant DEGs in 5w Aβ hiNSneurons, with APOE being the most significant upregulated gene. E: Neuronal gene ontology analysis in 3w/5w Aβ hiNSneurons. F: Direct comparison of neuronal DEGs depending on Ab or hiMG for ctrl and 3w Aβ hiNS shown in volcano plots. Top 10 DEGs in respect to fold change and/or adjusted pvalue are labeled. Note that AD-associated genes, such as CCL2, STAT3 and VIM, are only upregulated if hiMG were present during Aβ treatment
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 | 0.001 | 0.006 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.774 | 0.177 |
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".