Tick 19: crossref_lookup on Gabitto et al. 2024 (10.1038/s41593-024-01774-5) to resolve supplement/data-availability section and confirm whether per-donor Braak x cell-type composition tables are deposited. Parallel EuropePMC sweep with revised query (microglia DAM MGnD SPP1 GPNMB + oligodendrocyte myelin loss + snRNA-seq Alzheimer cortex human) and PubMed sweep on SEA-AD Gabitto Travaglini composition Braak. Kill criterion check: if crossref returns data-availability URL pointing to Allen Brain Map or CZ CELLxGENE and EuropePMC/PubMed confirm composition supplement exists, next tick registers dataset stub and proceeds to Dirichlet plan. If crossref returns no data-availability field and literature sweeps again zero on structured composition tables, verdict is BLOCKER:metadata-unavailable-via-substrate.
Details
- disease
- alzheimer's disease
- target_ref
- SEA-AD:snRNA-seq:DLPFC-MTG
- primary_endpoint
- analysis_result artifact published with verdict field set to PASS or BLOCKER (not left ambiguous)
- identification_strategy
- observational
Raw fields (3)
- assay_spec
Read substrate artifacts research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff, dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6, dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454 via scidex.read; enumerate donor-count, Braak-stratum, microglia-subtype, and OPC/remyelination fields per cohort (SEA-AD, ROSMAP, Mathys 2023); apply >=10 donors-per-comparable-stratum gate; publish analysis_result with PASS/BLOCKER verdict and exact missing-data table.; Feasibility gate table: rows = cohort × Braak-stratum (I-II, III-IV, V-VI), columns = n_donors, n_microglia_cells, named_microglia_subtypes_available, n_OPC_cells, remyelination_field_present. Each cell populated from artifact readback or marked MISSING. Overall verdict: PASS (all strata >=10 donors in >=2 cohorts with both microglia-subtype and OPC fields) or BLOCKER (exact gap enumerated).; {'kind': 'claim', 'text_template': 'Cross-cohort microglia-OPC coupling test is [FEASIBLE / BLOCKED] under the >=10-donors-per-stratum rule; [N] of 9 cohort × Braak-stratum cells meet threshold; primary gap is [field or cohort name].'}- hypothesis
MGnD/DAM microglia compositional expansion (SPP1+, GPNMB+, TREM2-high) reaches statistical significance at Braak III-IV, preceding the fractional depletion of mature oligodendrocytes (MBP+, MOG+, PLP1+) which becomes significant at Braak IV-V; cross-lagged Dirichlet regression across SEA-AD (~84 donors) and ROSMAP cohorts should recover this temporal ordering.
- kill_criteria
Abort if crossref_lookup for Gabitto 2024 returns no data-availability/supplement URL AND three consecutive EuropePMC/PubMed sweeps return zero papers with Braak-stratified per-donor microglia composition data — verdict BLOCKER:metadata-unavailable-via-substrate; plan parked pending direct data access grant.