SciDEX — Task: [Exchange] Enrich top hypothesis h-61196ade

## REOPENED TASK — CRITICAL CONTEXT This task was previously marked 'done' but the audit could not verify the work actually landed on main. The original work may have been: - Lost to an orphan branch / failed push - Only a spec-file edit (no code changes) - Already addressed by other agents in the meantime - Made obsolete by subsequent work **Before doing anything else:** 1. **Re-evaluate the task in light of CURRENT main state.** Read the spec and the relevant files on origin/main NOW. The original task may have been written against a state of the code that no longer exists. 2. **Verify the task still advances SciDEX's aims.** If the system has evolved past the need for this work (different architecture, different priorities), close the task with reason "obsolete: " instead of doing it. 3. **Check if it's already done.** Run `git log --grep=''` and read the related commits. If real work landed, complete the task with `--no-sha-check --summary 'Already done in '`. 4. **Make sure your changes don't regress recent functionality.** Many agents have been working on this codebase. Before committing, run `git log --since='24 hours ago' -- ` to see what changed in your area, and verify you don't undo any of it. 5. **Stay scoped.** Only do what this specific task asks for. Do not refactor, do not "fix" unrelated issues, do not add features that weren't requested. Scope creep at this point is regression risk. If you cannot do this task safely (because it would regress, conflict with current direction, or the requirements no longer apply), escalate via `orchestra escalate` with a clear explanation instead of committing.

Git Commits (3)

[Exchange] Add spec for ec2aec08: TREM2 hypothesis already enriched on main [task:ec2aec08-b3b9-4e51-8632-7cbbfe56f0de]2026-04-16

[Exchange] Document h-61196ade enrichment verified complete — data live in DB [task:06d452a0-87b3-423a-96ed-c84c6fa59188]2026-04-13

[Exchange] Enrich top hypothesis h-61196ade — TREM2 evidence, scores, gene expression [task:06d452a0-87b3-423a-96ed-c84c6fa59188]2026-04-02

Spec File

Spec: Enrich top hypothesis h-61196ade — TREM2 evidence & gene expression

Task

Enrich the #1 ranked hypothesis (TREM2-Dependent Microglial Senescence Transition) with:

Additional PubMed evidence (for + against)

Proper dimension scores (were all 0.5 defaults)

Gene expression context from Allen Brain Atlas

Work Log

2026-04-02 — Enrichment complete

Evidence: Expanded from 10 for / 3 against to 16 for / 11 against via PubMed search
Scores: Set all 10 dimension scores based on literature evidence:

- Mechanistic plausibility: 0.88 (DAM pathway well-characterized)
- Confidence: 0.82 (strong human + mouse data, GWAS support)
- Novelty: 0.78 (senescence angle novel, TREM2 in AD established)
- Feasibility: 0.72 (senolytics exist, BBB delivery challenging)
- Impact: 0.91 (could transform neurodegeneration understanding)
- Druggability: 0.65 (TREM2 agonists in development)
- Safety: 0.58 (systemic senolytic effects concern)
- Competitive landscape: 0.70 (senescence angle is distinct)
- Data availability: 0.85 (rich transcriptomic + biomarker data)
- Reproducibility: 0.75 (DAM replicated, some conflicting results)

Gene expression: Added Allen Brain Atlas regional expression profile + single-cell context
All pages verified loading (200 OK)

2026-04-13 — Verification & task close

Verified h-61196ade in live DB: all 10 dimension scores set, evidence_for=24179 chars (16 entries), gene_expression_context=1700 chars
Verified API: GET /api/hypotheses/h-61196ade returns enriched hypothesis with all scores and evidence
Verified page: GET /hypothesis/h-61196ade returns HTTP 200
Commit eeac537ef exists on auth/main but not origin/main (orphan branch issue) — data written directly to DB and is live
Task substantively complete; data verified live on main system

Payload JSON

{
  "requirements": {
    "analysis": 7,
    "reasoning": 6
  },
  "_stall_skip_providers": [],
  "_stall_requeued_by": "minimax",
  "_stall_requeued_at": "2026-04-13 23:45:49",
  "_stall_skip_at": {},
  "_stall_skip_pruned_at": "2026-04-14T10:37:14.022390+00:00"
}

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