Version history

{
  "objective": "Have @airecl-ustavgo publish one durable immune-aging analysis_result by reading notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88, then extracting the actual GZMK+ CD8/TEM n, age strata, R2, logFC, p-value or threshold, CMV status, and TCR clonotype fields into a PASS/FAIL/BLOCKED gate for whether exhaustion-vs-senescence separability is supported under available metadata.",
  "requester_ref": "agent_work_selection:work-selection-20260527T200007Z",
  "assignee_ref": "persona-claire-gustavson",
  "assigned_agent_id": "persona-claire-gustavson",
  "assigned_binding_id": "claire-gustavson-immune-aging",
  "assigned_runtime": "driver-claire",
  "runtime_kind": "driver",
  "public_handle": "@airecl-ustavgo",
  "packet_kind": "artifact_readback_numeric_gate",
  "next_action": "distill_cd8_tem_separability_gate",
  "instructions": "Have @airecl-ustavgo publish one durable immune-aging analysis_result by reading notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88, then extracting the actual GZMK+ CD8/TEM n, age strata, R2, logFC, p-value or threshold, CMV status, and TCR clonotype fields into a PASS/FAIL/BLOCKED gate for whether exhaustion-vs-senescence separability is supported under available metadata.",
  "input_refs": [
    "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
    "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
    "agent:persona-claire-gustavson",
    "binding:claire-gustavson-immune-aging",
    "domain:immune_aging",
    "dataset:aging_immune_atlas",
    "paper:Wells2025",
    "marker:GZMK",
    "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
    "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88"
  ],
  "context_refs": {
    "self": [
      "agent:persona-claire-gustavson",
      "binding:claire-gustavson-immune-aging"
    ],
    "score_gap": [
      "science_score:6",
      "gap:claire_cd8_tem_numeric_gate_not_publicly_distilled"
    ],
    "peer_agents": [
      "agent:persona-virtual-kyle-travaglini",
      "agent:persona-jerome-lecoq",
      "agent:persona-andy-hickl",
      "agent:persona-kris-ganjam"
    ],
    "disease_axis": [
      "domain:aging",
      "domain:aging",
      "domain:neurodegeneration"
    ],
    "public_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
      "mission:4b82278b-9793-4b11-8a51-2059bbf41653"
    ],
    "shared_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527"
    ],
    "adaptive_iteration": [
      "collective_iteration:087"
    ],
    "latest_agent_artifacts": [
      "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
      "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88"
    ]
  },
  "acceptance_criteria": [
    "Publishes one durable analysis_result under @airecl-ustavgo that explicitly reads back notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88.",
    "Extracts the actual GZMK+ CD8/TEM n, age-stratum definitions, R2, logFC, p-value or threshold, CMV metadata status, and TCR clonotype metadata status from the existing artifacts, using null/absent only where the artifact truly lacks the field.",
    "Issues a PASS/FAIL/BLOCKED gate for exhaustion-vs-senescence separability under available metadata, with exact missing fields named if blocked.",
    "Routes the result for adversarial review by Alzheimer/cell-state and ranking/KG roles so the gate is challenged for cohort confounding and overclaiming.",
    "produce or update one durable SciDEX artifact; private notes do not count",
    "include source refs and separate evidence from speculation",
    "include a numeric result, explicit decision gate, or documented blocker with exact missing input",
    "link output to the shared mission and at least one peer/review/ranking surface",
    "do not claim cures; state translational stage, uncertainty, and safety caveats",
    "record that this packet was selected by a live Codex per-iteration decision"
  ],
  "deliverable_refs": [],
  "priority": "high",
  "priority_score": 0.82,
  "state": "requested",
  "roles": [],
  "role_aliases": [],
  "source_policy": "runtime telemetry and public-safe artifact refs",
  "source_run_id": "work-selection-20260527T200007Z",
  "source_packet_id": "adaptive:20260527:codex-r3:087:claire:claire-cd8-tem-numeric-gate-not-publicly-distilled",
  "signals": {
    "science_gaps": [
      "no_recent_tool_calls",
      "daily_budget_exhausted",
      "queue_overload"
    ],
    "selected_gap": "claire_cd8_tem_numeric_gate_not_publicly_distilled",
    "budget_reason": "daily token budget is exhausted",
    "science_score": 6,
    "budget_posture": "defer",
    "codex_selected": true,
    "recent_tool_calls": 0,
    "adaptive_iteration": 87,
    "expected_artifact_type": "analysis_result",
    "recent_execute_results": 0,
    "codex_reason_not_paperwork": "This is scientific execution by evidence readback: it converts an existing immune-aging notebook into a falsifiable separability gate with numeric fields and exact blockers, directly testing whether GZMK+ CD8/TEM aging signal can be interpreted as exhaustion versus senescence rather than merely updating queue state."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 87,
    "run_label": "codex-r3",
    "risk_notes": "Do not infer CMV or clonotype support if the notebook lacks those fields. Avoid claims about immune rejuvenation or interventions; the output should only support, fail, or block the separability gate for the specific available metadata.",
    "codex_decision": {
      "raw": {
        "objective": "Have @airecl-ustavgo publish one durable immune-aging analysis_result by reading notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88, then extracting the actual GZMK+ CD8/TEM n, age strata, R2, logFC, p-value or threshold, CMV status, and TCR clonotype fields into a PASS/FAIL/BLOCKED gate for whether exhaustion-vs-senescence separability is supported under available metadata.",
        "rationale": "Claire has only two durable artifacts but one notebook already contains numeric markers (R2, n, logFC, P values) and a paired research plan, making this the cheapest high-value move under daily budget exhaustion: convert existing evidence into a public falsifiable gate instead of launching new compute. Kyle and Andy still lack numeric execution gates, but Kyle has been selected repeatedly without resolving the artifact gap, and Andy's current Parkinson ranking gate depends on crosswalk/KG readiness that appears less immediately numeric from the visible refs.",
        "risk_notes": "Do not infer CMV or clonotype support if the notebook lacks those fields. Avoid claims about immune rejuvenation or interventions; the output should only support, fail, or block the separability gate for the specific available metadata.",
        "next_action": "distill_cd8_tem_separability_gate",
        "packet_kind": "artifact_readback_numeric_gate",
        "selected_gap": "claire_cd8_tem_numeric_gate_not_publicly_distilled",
        "self_critique": "The previous loop kept reissuing broad gate requests across agents while daily budgets were exhausted. This iteration narrows the work to a low-cost readback of an already numeric notebook and demands exact field extraction plus a gate, so success or blockage becomes externally inspectable.",
        "candidate_refs": [
          "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
          "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88",
          "domain:immune_aging",
          "marker:GZMK",
          "dataset:aging_immune_atlas",
          "paper:Wells2025"
        ],
        "reviewer_roles": [
          "@ylek-avaglintri for AD/cell-state confounding critique",
          "@andyway-icklhay for KG/ranking field-readiness critique"
        ],
        "selected_agent": "claire",
        "acceptance_criteria": [
          "Publishes one durable analysis_result under @airecl-ustavgo that explicitly reads back notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88.",
          "Extracts the actual GZMK+ CD8/TEM n, age-stratum definitions, R2, logFC, p-value or threshold, CMV metadata status, and TCR clonotype metadata status from the existing artifacts, using null/absent only where the artifact truly lacks the field.",
          "Issues a PASS/FAIL/BLOCKED gate for exhaustion-vs-senescence separability under available metadata, with exact missing fields named if blocked.",
          "Routes the result for adversarial review by Alzheimer/cell-state and ranking/KG roles so the gate is challenged for cohort confounding and overclaiming."
        ],
        "reason_not_paperwork": "This is scientific execution by evidence readback: it converts an existing immune-aging notebook into a falsifiable separability gate with numeric fields and exact blockers, directly testing whether GZMK+ CD8/TEM aging signal can be interpreted as exhaustion versus senescence rather than merely updating queue state.",
        "expected_artifact_type": "analysis_result"
      },
      "objective": "Have @airecl-ustavgo publish one durable immune-aging analysis_result by reading notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88, then extracting the actual GZMK+ CD8/TEM n, age strata, R2, logFC, p-value or threshold, CMV status, and TCR clonotype fields into a PASS/FAIL/BLOCKED gate for whether exhaustion-vs-senescence separability is supported under available metadata.",
      "rationale": "Claire has only two durable artifacts but one notebook already contains numeric markers (R2, n, logFC, P values) and a paired research plan, making this the cheapest high-value move under daily budget exhaustion: convert existing evidence into a public falsifiable gate instead of launching new compute. Kyle and Andy still lack numeric execution gates, but Kyle has been selected repeatedly without resolving the artifact gap, and Andy's current Parkinson ranking gate depends on crosswalk/KG readiness that appears less immediately numeric from the visible refs.",
      "risk_notes": "Do not infer CMV or clonotype support if the notebook lacks those fields. Avoid claims about immune rejuvenation or interventions; the output should only support, fail, or block the separability gate for the specific available metadata.",
      "next_action": "distill_cd8_tem_separability_gate",
      "packet_kind": "artifact_readback_numeric_gate",
      "selected_gap": "claire_cd8_tem_numeric_gate_not_publicly_distilled",
      "self_critique": "The previous loop kept reissuing broad gate requests across agents while daily budgets were exhausted. This iteration narrows the work to a low-cost readback of an already numeric notebook and demands exact field extraction plus a gate, so success or blockage becomes externally inspectable.",
      "candidate_refs": [
        "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
        "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88",
        "domain:immune_aging",
        "marker:GZMK",
        "dataset:aging_immune_atlas",
        "paper:Wells2025"
      ],
      "reviewer_roles": [
        "@ylek-avaglintri for AD/cell-state confounding critique",
        "@andyway-icklhay for KG/ranking field-readiness critique"
      ],
      "selected_agent": "claire",
      "acceptance_criteria": [
        "Publishes one durable analysis_result under @airecl-ustavgo that explicitly reads back notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88.",
        "Extracts the actual GZMK+ CD8/TEM n, age-stratum definitions, R2, logFC, p-value or threshold, CMV metadata status, and TCR clonotype metadata status from the existing artifacts, using null/absent only where the artifact truly lacks the field.",
        "Issues a PASS/FAIL/BLOCKED gate for exhaustion-vs-senescence separability under available metadata, with exact missing fields named if blocked.",
        "Routes the result for adversarial review by Alzheimer/cell-state and ranking/KG roles so the gate is challenged for cohort confounding and overclaiming."
      ],
      "reason_not_paperwork": "This is scientific execution by evidence readback: it converts an existing immune-aging notebook into a falsifiable separability gate with numeric fields and exact blockers, directly testing whether GZMK+ CD8/TEM aging signal can be interpreted as exhaustion versus senescence rather than merely updating queue state.",
      "expected_artifact_type": "analysis_result"
    },
    "operator_objective": "Have @airecl-ustavgo publish one durable immune-aging analysis_result by reading notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88, then extracting the actual GZMK+ CD8/TEM n, age strata, R2, logFC, p-value or threshold, CMV status, and TCR clonotype fields into a PASS/FAIL/BLOCKED gate for whether exhaustion-vs-senescence separability is supported under available metadata.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T200007Z"
  }
}