review-zoom-14-gene-background

Metadata

Status	done
Assigned	`agent-972`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-05-06T20:28:34.839271224+00:00
Started	2026-05-06T20:44:14.525120574+00:00
Completed	2026-05-06T20:56:46.855868166+00:00
Tags	`bog-this-week`, `bog-deck`, `review-zoom`, `revision-fanout`, `git-provenance`, `eval-scheduled`
Eval score	0.95
└ blocking impact	0.95
└ completeness	0.96
└ coordination overhead	0.97
└ correctness	0.94
└ downstream usability	0.97
└ efficiency	0.91
└ intent fidelity	0.91
└ style adherence	0.96

Description

User review points 19, 20, 21 and overall gene-background note.

Goal: replace the weak DUX4/D4Z4 slidelet, keep/improve the strong OR4F slidelet, and improve TAR1 readability and background. The zoom review should answer: What is DUX4? What is OR4F? What is TAR1? Why do they matter in PHRs?

Critical provenance requirement:

First read the upstream review-zoom-git-provenance-audit output and use git history to identify which gene-biology assets/scripts were generated, copied, or cropped, and when.

Requirements:

Inspect existing slide 14 source assets/scripts plus ED3/ED4 figures/captions and relevant literature/survey notes already in the repo.
For DUX4/D4Z4: produce a slidelet with actual information, not just decorative context. Include FSHD/D4Z4 macrosatellite relevance only insofar as it supports the PHR story.
For OR4F: preserve the useful pseudogenization gradient and connect to gene enrichment outputs where possible.
For TAR1: improve readability; avoid hard-to-read text-on-image overlays; explain TAR1/subtelomeric repeat relevance in plain terms.
Keep outputs isolated.

Deliverables:

Three short slidelet specs or candidate assets under slides/v2-review-zoom/_revision_assets/14_gene_background/.
Markdown with source citations/paths, git provenance, and speaker notes.

User review points 19, 20, 21 and overall gene-background note.

Goal: replace the weak DUX4/D4Z4 slidelet, keep/improve the strong OR4F slidelet, and improve TAR1 readability and background. The zoom review should answer: What is DUX4? What is OR4F? What is TAR1? Why do they matter in PHRs?

Critical provenance requirement:
- First read the upstream `review-zoom-git-provenance-audit` output and use git history to identify which gene-biology assets/scripts were generated, copied, or cropped, and when.

Requirements:
- Inspect existing slide 14 source assets/scripts plus ED3/ED4 figures/captions and relevant literature/survey notes already in the repo.
- For DUX4/D4Z4: produce a slidelet with actual information, not just decorative context. Include FSHD/D4Z4 macrosatellite relevance only insofar as it supports the PHR story.
- For OR4F: preserve the useful pseudogenization gradient and connect to gene enrichment outputs where possible.
- For TAR1: improve readability; avoid hard-to-read text-on-image overlays; explain TAR1/subtelomeric repeat relevance in plain terms.
- Keep outputs isolated.

Deliverables:
- Three short slidelet specs or candidate assets under `slides/v2-review-zoom/_revision_assets/14_gene_background/`.
- Markdown with source citations/paths, git provenance, and speaker notes.

Depends on

Required by

Log

2026-05-06T20:28:34.808191499+00:00 Task paused
2026-05-06T20:28:35.239685978+00:00 Task published
2026-05-06T20:44:14.525124972+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-05-06T20:44:37.046886145+00:00 Starting documentation pass: reading provenance audit, current slide 14 assets, and related manuscript/figure notes before writing isolated revision assets.
2026-05-06T20:46:48.881794729+00:00 FANOUT_DECISION: stay inline — deliverable is isolated documentation/spec files under one revision-assets directory; splitting would create coordination overhead without independent write scopes.
2026-05-06T20:55:10.411951835+00:00 Drafted isolated slide 14 gene-background revision assets: DUX4/D4Z4, OR4F, TAR1 specs plus synthesis README with source paths, git provenance, and speaker notes.
2026-05-06T20:56:14.206528877+00:00 Validated: deliverables are isolated under slides/v2-review-zoom/_revision_assets/14_gene_background; include three slidelet specs plus README with citations, git provenance, and speaker notes. git diff --cached --check passed; cited repo paths exist; ASCII/trailing whitespace checks passed. Docs-only task, so cargo build/test not run.
2026-05-06T20:56:35.636071172+00:00 Committed: cda3b92 — pushed to origin/wg/agent-972/review-zoom-14-gene-background
2026-05-06T20:56:46.855876502+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-06T21:11:02.852277550+00:00 PendingEval → Done (evaluator passed; downstream unblocks)