JSON Snapshot
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PNI` 组长期全因死亡风险最高（adjusted HR 2.26），基线心衰负担与 `CHD Only` 组同属最高层。项目状态前推到 `figures` 前置阶段，同时保留 `analysis_ready_v2` fully adjusted 重跑作为非阻塞增强项。"], "figure_review": {"ai_review_status": "", "visual_gate_status": "", "human_review_status": ""}, "reference_review": {"benchmark_status": "", "official_source_status": ""}, "automation": {}, "children": [], "detail_json": "state/projects/A014-coronary-inflammatory-nutrition-nhanes.json"}, {"project_id": "A015-cardiovascular-prism-nhanes", "project_label": "A015-cardiovascular-prism-nhanes", "project_type": "article", "path": "/Users/terry/ai-research-army-codex/clients/A015-cardiovascular-prism-nhanes", "state_path": "/Users/terry/ai-research-army-codex/clients/A015-cardiovascular-prism-nhanes/state.yaml", "board_path": "/Users/terry/ai-research-army-codex/clients/A015-cardiovascular-prism-nhanes/board.md", "progress_path": "/Users/terry/ai-research-army-codex/clients/A015-cardiovascular-prism-nhanes/progress.md", "todo_path": 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"blocker_summary": {}, "human_gate_required": false, "machine_fixable_blockers": false, "active_work_items": {"in_progress": 0, "pending": 2, "blocked": 0}, "completed_steps": ["initialization", "requirement_lock", "research_design", "data_acquisition", "data_profiling", "data_forensics", "statistical_analysis", "figures", "literature"], "pending_steps": ["manuscript", "review", "submission", "delivery"], "next_legal_action": "promote_package_mode_after_closure", "recent_updates": ["2026-04-14 23:32: Ming 完成 `01_prepare_data.py`，生成 `analysis_ready.csv`、`cohort_definition.md`、`data_dictionary.md` 与 `data_profile_trace.json`，项目切换到 `data_forensics`", "2026-04-15 00:00: Ming + Alex 完成 `01b_data_forensics.py`，确认 A015 结构性检查为 `GREEN`；仅 20 行缺失 mortality follow-up，已登记为 Cox 阶段常规排除，不阻塞统计推进", "2026-04-15 11:14: Kenji 新增并跑通 `scripts/02_analysis.R`，将 `CVD anchor` 修正为 HF-safe `coronary_history OR stroke_history` 以避免与基线 HF 结局重叠；quality A/B 主分析显示 `CVD + PRISm` 组基线 HF burden `OR 18.83 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"statistical_analysis", "figures", "literature"], "pending_steps": ["manuscript", "review", "submission", "delivery"], "next_legal_action": "promote_package_mode_after_closure", "recent_updates": ["2026-04-14 23:32: Wei 校验 raw bundle，确认 A010 core files + BPQ/DIQ/ALQ/PAQ 已全部到位，项目从 `data_acquisition` 推进到 `data_profiling`", "2026-04-15 09:54: Ming 完成 `scripts/01_prepare_data.py`，生成 `analysis_ready.csv`、`cohort_definition.md`、`data_dictionary.md` 与 `data_profile_trace.json`；strict occult 实测 `n=424 / deaths=149 / HF=113`，relaxed occult 实测 `n=497 / deaths=165 / HF=134`，项目推进到 `data_forensics`", "2026-04-15 07:34: Ming + Alex 完成 `scripts/01b_data_forensics.py`，`outputs/ming/data_forensics_report.md` 判定 `GREEN`；strict primary / relaxed sensitivity 对齐无断裂，项目切换到 `statistical_analysis`", "2026-04-15 07:44: Kenji 完成 `scripts/02_analysis.R`，输出 `analysis_results.md`、`model_estimates.csv`、`table1.csv` 与 `analysis_trace.json`；quality A/B strict primary 显示 occult abnormal 关联更高全因死亡风险 `adjusted HR 2.75 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4-level severity，项目切换到 `data_forensics`", "2026-04-15 06:50: Ming + Alex 完成 `01b_data_forensics.py`，确认 A017 结构性检查为 `GREEN`；4-level severity 到 3-level fallback 映射完整，moderate-severe tail cell 记为 `watch` 但不构成 data forensics blocker；项目推进到 `statistical_analysis`", "2026-04-15 10:43: Kenji 完成 `scripts/02_analysis.R`，输出 `analysis_results.md`、`model_estimates.csv`、`table1.csv`、`severity_group_prevalence.csv` 与 `analysis_trace.json`；4-level primary 显示 `PRISm` 死亡风险 `HR 2.40 (1.23-4.66)`、`moderate-severe obstruction` 死亡风险 `HR 2.03 (1.01-4.06)` 且基线 HF burden `OR 2.64 (1.00-6.97)`，3-level fallback `obstruction` 亦保持死亡风险升高 `HR 1.79 (1.03-3.10)`；项目合法推进到 `figures`", "2026-04-15 12:33: Lena 完成 `scripts/03_figures.R`，生成 `figure1_severity_burden_panels`、`figure2_severity_risk_forest`、`figure3_severity_clinical_heatmap` 与 `figureS1_severity_fallback_forest`（PNG/TIFF），并写入 `outputs/lena/figure_storyboard.md` 与 `outputs/traces/figure_review_trace.json`；primary 4-level severity 梯度与 3-level fallback robustness 现已图形化固定，项目合法推进到 `literature`", "2026-04-15 14:04: Jing 新增并跑通 `scripts/04_build_literature_pool.py`，复用 shared verified pool 固化 `27` 篇文献，输出 `outputs/verified_ref_pool.json`、`outputs/jing/literature_summary.md` 与 `outputs/jing/literature_review_gate.md`；slot 3 合法推进到 `manuscript`，并要求写稿时同时保留 `4-level primary` 与 `3-level fallback` 稳健性叙事"], "figure_review": {"ai_review_status": "pending", "visual_gate_status": "", "human_review_status": "pending"}, "reference_review": {"benchmark_status": "", "official_source_status": ""}, "automation": {}, "children": [], "detail_json": "state/projects/A017-cardiovascular-airflow-severity-nhanes.json"}, {"project_id": "A018-hysterectomy-mortality-nhanes", "project_label": "A018-hysterectomy-mortality-nhanes", "project_type": "article", "path": "/Users/terry/ai-research-army-codex/clients/A018-hysterectomy-mortality-nhanes", "state_path": "/Users/terry/ai-research-army-codex/clients/A018-hysterectomy-mortality-nhanes/state.yaml", "board_path": 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"open_blockers": [{"id": "author-metadata-finalization", "title": "Real authors, affiliations, and corresponding-author details remain placeholders", "class": "human_review_blocker", "status": "open", "source": "blockers", "owner": "Operator", "machine_fixable": false, "requires_human": true, "resolution_protocol": "human_gate", "evidence": ["submission_package/title_page.md"]}, {"id": "cover-letter-confirmations", "title": "Final submission confirmations in cover letter still require operator sign-off", "class": "human_review_blocker", "status": "open", "source": "blockers", "owner": "Operator", "machine_fixable": false, "requires_human": true, "resolution_protocol": "human_gate", "evidence": ["submission_package/cover_letter.md"]}], "blocker_summary": {"human_review_blocker": 2}, "human_gate_required": true, "machine_fixable_blockers": false, "active_work_items": {"in_progress": 0, "pending": 1, "blocked": 0}, "completed_steps": ["initialization", "scope_lock", "data_acquisition", "data_profiling", "data_forensics", "research_design", "statistical_analysis", "literature", "figures", "manuscript", "review", "submission", "delivery"], "pending_steps": ["author_metadata_fill", "figure_final_human_gate", "operator_submission"], "next_legal_action": "wait_human_or_external_truth", "recent_updates": [], "figure_review": {"ai_review_status": "pass", "visual_gate_status": "approved", "human_review_status": "approved"}, "reference_review": {"benchmark_status": "pass", "official_source_status": "pass"}, "automation": {}, "children": [], "detail_json": "state/projects/A018-hysterectomy-mortality-nhanes.json"}, {"project_id": "A019-liposomal-bupivacaine-anorectal-recovery-meta", "project_label": "Liposomal Bupivacaine for Early Recovery After Hemorrhoidectomy", "project_type": "article", "path": "/Users/terry/ai-research-army-codex/clients/A019-liposomal-bupivacaine-anorectal-recovery-meta", "state_path": "/Users/terry/ai-research-army-codex/clients/A019-liposomal-bupivacaine-anorectal-recovery-meta/project_manifest.yaml", "board_path": "/Users/terry/ai-research-army-codex/clients/A019-liposomal-bupivacaine-anorectal-recovery-meta/board.md", "progress_path": "/Users/terry/ai-research-army-codex/clients/A019-liposomal-bupivacaine-anorectal-recovery-meta/progress.md", "todo_path": "/Users/terry/ai-research-army-codex/clients/A019-liposomal-bupivacaine-anorectal-recovery-meta/todo.md", "created_at": "2026-04-15 11:56", "updated_at": "2026-04-15T14:24:11+08:00", "phase": "review", "status": "active", "pause_reason": "", "package_mode": "draft", "target_journal": "Techniques in Coloproctology", "target_tier": "Tier2-Tier3", "bucket": "repair_machine_fixable_blockers", "editorial_verdict": "BLOCK", "editorial_next_action": "repair_machine_fixable_blockers", "manifest_errors": [], "manifest_warnings": [], "open_blocker_count": 0, "open_blockers": [], "blocker_summary": {}, "human_gate_required": false, "machine_fixable_blockers": false, "active_work_items": {"in_progress": 0, "pending": 1, "blocked": 0}, "completed_steps": ["initialization", "scope_lock", "data_acquisition", "data_profiling", "research_design", "statistical_analysis", "literature", "figures", "manuscript"], "pending_steps": ["review", "submission", "delivery"], "next_legal_action": "repair_machine_fixable_blockers", "recent_updates": [], "figure_review": {"ai_review_status": "pending", "visual_gate_status": "pending", "human_review_status": "pending"}, "reference_review": {"benchmark_status": "pass", "official_source_status": "pass"}, "automation": {}, "children": [], "detail_json": "state/projects/A019-liposomal-bupivacaine-anorectal-recovery-meta.json"}, {"project_id": "M001-cardiopulmonary-matrix-x4", "project_label": "心血管疾病史 × 异常肺功能/气流阻塞 × 心衰负担/死亡风险", "project_type": "matrix_parent", "path": "/Users/terry/ai-research-army-codex/clients/M001-cardiopulmonary-matrix-x4", "state_path": "/Users/terry/ai-research-army-codex/clients/M001-cardiopulmonary-matrix-x4/state.yaml", "board_path": "/Users/terry/ai-research-army-codex/clients/M001-cardiopulmonary-matrix-x4/board.md", "progress_path": "/Users/terry/ai-research-army-codex/clients/M001-cardiopulmonary-matrix-x4/progress.md", "todo_path": "/Users/terry/ai-research-army-codex/clients/M001-cardiopulmonary-matrix-x4/todo.md", "created_at": "2026-04-14 22:25", "updated_at": "2026-04-15T14:24:11+08:00", "phase": "child_literature", "status": "active", "pause_reason": "", "package_mode": "", "target_journal": "", "target_tier": "", "bucket": "repair_manifest_contract", "editorial_verdict": "SKIP", "editorial_next_action": "continue_pipeline", "manifest_errors": ["lifecycle.phase/current_phase 非法值: 'child_literature'，允许: ['crystallizing', 'data-explore', 'data-forensics', 'delivery', 'executing', 'figures', 'intake', 'literature', 'manuscript', 'planning', 'published', 'research-design', 'retro', 'review', 'reviewing', 'risk-assess', 'statistics', 'submission', 'submitting']"], "manifest_warnings": [], "open_blocker_count": 0, "open_blockers": [], "blocker_summary": {}, "human_gate_required": false, "machine_fixable_blockers": false, "active_work_items": {"in_progress": 0, "pending": 3, "blocked": 0}, "completed_steps": ["initialization", "shared_preflight_kickoff", "slot_freeze", "shared_literature", "shared_dataset_mapping", "shared_design_d1", "child_data_acquisition", "child_data_profiling", "child_data_forensics", "child_statistical_analysis", "child_figures"], "pending_steps": ["child_literature", "child_manuscript", "child_review", "child_submission"], "next_legal_action": "启动 A016 的结果驱动 literature review，围绕 hidden-risk mortality framing 整理 must-cite 池；A015 与 A017 已进入 manuscript first-draft preflight；A010 继续等待真实作者 metadata 与最终图审签发", "recent_updates": ["2026-04-15 11:14: Kenji 完成 A015 `scripts/02_analysis.R`，识别并修复了 `CVD anchor` 含既往 HF 导致基线 HF 结局与暴露重叠的问题，改用 HF-safe `coronary_history OR stroke_history` 主线；quality A/B 主分析显示 `CVD + PRISm` 组基线 HF burden `OR 18.83`、全因死亡风险 `HR 2.27`，slot 2 合法推进到 `figures`，matrix 正式切换到 `child_figures`", "2026-04-15 12:02: Lena 完成 A015 `scripts/03_figures.R`，slot 2 生成 `figure1_joint_prism_burden_panels`、`figure2_joint_prism_risk_forest`、`figure3_joint_prism_clinical_heatmap` 与 `figureS1_joint_prism_sensitivity_forest`（PNG/TIFF），并写入 `figure_storyboard.md` 与 `figure_review_trace.json`；slot 2 合法推进到 `literature`，matrix 继续保持 `child_figures`，因为 A017 出图仍是当前 gating lane", "2026-04-15 12:33: Lena 完成 A017 `scripts/03_figures.R`，slot 3 生成 `figure1_severity_burden_panels`、`figure2_severity_risk_forest`、`figure3_severity_clinical_heatmap` 与 `figureS1_severity_fallback_forest`（PNG/TIFF），并写入 `outputs/lena/figure_storyboard.md` 与 `outputs/traces/figure_review_trace.json`；至此 A015/A016/A017 已全部进入 `literature`，matrix 正式切换到 `child_literature`", "2026-04-15 13:24: Jing 完成 A015 `scripts/04_build_literature_pool.py`，围绕 HF-safe CVD + PRISm 高 burden / mortality 主线固化 `27` 篇 verified references，并写出 `outputs/verified_ref_pool.json`、`outputs/jing/literature_summary.md` 与 `outputs/jing/literature_review_gate.md`；slot 2 合法推进到 `manuscript`，matrix 继续保持 `child_literature`，因为 A016/A017 仍在 literature 阶段", "2026-04-15 14:04: Jing 完成 A017 `scripts/04_build_literature_pool.py`，围绕 severity gradient + fallback robustness 主线固化 `27` 篇 verified references，并写出 `outputs/verified_ref_pool.json`、`outputs/jing/literature_summary.md` 与 `outputs/jing/literature_review_gate.md`；slot 3 合法推进到 `manuscript`，matrix 继续保持 `child_literature`，因为 A016 仍在 literature 阶段"], "figure_review": {"ai_review_status": "", "visual_gate_status": "", "human_review_status": ""}, "reference_review": {"benchmark_status": "", "official_source_status": ""}, "automation": {"id": "x4", "name": "心肺矩阵论文 x4", "status": "active", "cadence": "每 10 分钟", "workspace": "/Users/terry/ai-research-army-codex", "objective": "持续扫描矩阵项目，推进下一个合法 pipeline step，修复 machine-fixable blocker，并把摘要结果发到 inbox"}, "children": [{"slot": 1, "project_id": "A010-coronary-airflow-nhanes", "status": "draft_package_ready", "current_phase": "delivery", "rank": 1, "first_priority": true, "path": "/Users/terry/ai-research-army-codex/clients/A010-coronary-airflow-nhanes"}, {"slot": 2, "project_id": "A015-cardiovascular-prism-nhanes", "status": "active", "current_phase": "manuscript", "rank": 2, "first_priority": false, "path": "/Users/terry/ai-research-army-codex/clients/A015-cardiovascular-prism-nhanes"}, {"slot": 3, "project_id": "A017-cardiovascular-airflow-severity-nhanes", "status": "active", "current_phase": "manuscript", "rank": 3, "first_priority": false, "path": "/Users/terry/ai-research-army-codex/clients/A017-cardiovascular-airflow-severity-nhanes"}, {"slot": 4, "project_id": "A016-cardiovascular-occult-lung-dysfunction-nhanes", "status": "active", "current_phase": "literature", "rank": 4, "first_priority": false, "path": "/Users/terry/ai-research-army-codex/clients/A016-cardiovascular-occult-lung-dysfunction-nhanes"}], "detail_json": "state/projects/M001-cardiopulmonary-matrix-x4.json"}, {"project_id": "M002-traditional-cardiac-matrix-x4", "project_label": "冠脉疾病锚点 × 多器官储备受损 × 心衰负担/长期死亡风险", "project_type": "matrix_parent", "path": "/Users/terry/ai-research-army-codex/clients/M002-traditional-cardiac-matrix-x4", "state_path": "/Users/terry/ai-research-army-codex/clients/M002-traditional-cardiac-matrix-x4/state.yaml", "board_path": "/Users/terry/ai-research-army-codex/clients/M002-traditional-cardiac-matrix-x4/board.md", "progress_path": "/Users/terry/ai-research-army-codex/clients/M002-traditional-cardiac-matrix-x4/progress.md", "todo_path": "/Users/terry/ai-research-army-codex/clients/M002-traditional-cardiac-matrix-x4/todo.md", "created_at": "2026-04-15 10:05", "updated_at": "2026-04-15T14:24:11+08:00", "phase": "statistics", "status": "active", "pause_reason": "", "package_mode": "", "target_journal": "", "target_tier": "", "bucket": "continue_pipeline", "editorial_verdict": "SKIP", "editorial_next_action": "continue_pipeline", "manifest_errors": [], "manifest_warnings": [], "open_blocker_count": 0, "open_blockers": [], "blocker_summary": {}, "human_gate_required": false, "machine_fixable_blockers": false, "active_work_items": {"in_progress": 0, "pending": 0, "blocked": 0}, "completed_steps": ["initialization", "slot_freeze", "child_research_design", "child_data_acquisition", "child_data_profiling", "child_data_forensics"], "pending_steps": ["child_statistical_analysis", "child_figures", "child_literature", "child_manuscript", "child_review", "child_submission"], "next_legal_action": "先推进 A011 > A012 的 Kenji weighted Table 1、baseline HF burden logistic 与 all-cause mortality Cox；并行放行 A013 与 A014 的 figures/literature 前置包装，暂不等待 fully adjusted v2", "recent_updates": [], "figure_review": {"ai_review_status": "", "visual_gate_status": "", "human_review_status": ""}, "reference_review": {"benchmark_status": "", "official_source_status": ""}, "automation": {"id": "automation", "name": "传统心外科矩阵 x4", "status": "paused", "cadence": "每 30 分钟", "workspace": "/Users/terry/ai-research-army-codex", "objective": "持续扫描矩阵项目，推进下一个合法 pipeline step，修复 machine-fixable blocker，并把摘要结果发到 inbox"}, "children": [{"slot": 1, "project_id": "A014-coronary-inflammatory-nutrition-nhanes", "status": "active", "current_phase": "figures", "rank": 1, "first_priority": true, "path": "/Users/terry/ai-research-army-codex/clients/A014-coronary-inflammatory-nutrition-nhanes"}, {"slot": 2, "project_id": "A013-coronary-hematologic-reserve-nhanes", "status": "active", "current_phase": "figures", "rank": 2, "first_priority": false, "path": "/Users/terry/ai-research-army-codex/clients/A013-coronary-hematologic-reserve-nhanes"}, {"slot": 3, "project_id": "A011-coronary-renal-reserve-nhanes", "status": "active", "current_phase": "statistical_analysis", "rank": 3, "first_priority": false, "path": "/Users/terry/ai-research-army-codex/clients/A011-coronary-renal-reserve-nhanes"}, {"slot": 4, "project_id": "A012-coronary-hepatic-reserve-nhanes", "status": "active", "current_phase": "statistical_analysis", "rank": 4, "first_priority": false, "path": "/Users/terry/ai-research-army-codex/clients/A012-coronary-hepatic-reserve-nhanes"}], "detail_json": "state/projects/M002-traditional-cardiac-matrix-x4.json"}]}