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, extracting the actual GZMK+ CD8/TEM n, age-stratum, R2, logFC, p-value or threshold, CMV, and TCR clonotype fields, then issuing a pass/fail/blocked gate for whether exhaustion-vs-senescence separability is supported under the 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, extracting the actual GZMK+ CD8/TEM n, age-stratum, R2, logFC, p-value or threshold, CMV, and TCR clonotype fields, then issuing a pass/fail/blocked gate for whether exhaustion-vs-senescence separability is supported under the 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:071"
    ],
    "latest_agent_artifacts": [
      "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
      "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88"
    ]
  },
  "acceptance_criteria": [
    "Read back notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88 before writing, rather than relying on titles or prior summaries.",
    "Extract explicit values or exact absence for GZMK+ CD8/TEM sample size, age strata, R2, logFC, p-value or threshold, CMV field, and TCR clonotype field.",
    "Publish one durable analysis_result with a pass/fail/blocked separability gate for exhaustion-vs-senescence, including the precise blocker if CMV or clonotype metadata are missing.",
    "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-r3:071: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": 71,
    "expected_artifact_type": "analysis_result",
    "recent_execute_results": 0,
    "codex_reason_not_paperwork": "This directly converts an executed immune-aging notebook into a falsifiable biological interpretation gate with named numeric fields and metadata blockers; it is not queue cleanup or planning."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 71,
    "run_label": "codex-r3",
    "risk_notes": "Do not infer CMV or clonotype separability if those fields are absent. Treat GZMK+ CD8/TEM age association as cohort- and metadata-limited, not as evidence of rejuvenation, therapy, or clinical benefit.",
    "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, extracting the actual GZMK+ CD8/TEM n, age-stratum, R2, logFC, p-value or threshold, CMV, and TCR clonotype fields, then issuing a pass/fail/blocked gate for whether exhaustion-vs-senescence separability is supported under the available metadata.",
        "rationale": "Claire has only two durable artifacts, but the notebook already carries numeric markers and execution markers, making a low-token readback-and-distillation likely to produce a public scientific gate despite exhausted daily budgets. Kyle and Andy still lack numeric or executed gate evidence, while Jerome and Kris have more existing execution output and were selected very recently for similar distillation work.",
        "risk_notes": "Do not infer CMV or clonotype separability if those fields are absent. Treat GZMK+ CD8/TEM age association as cohort- and metadata-limited, not as evidence of rejuvenation, therapy, or clinical benefit.",
        "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": "Previous loops repeatedly scheduled broad gate work without forcing exact value readback into a durable public result. This packet narrows the work to extracting named fields from two refs and publishing a concrete pass/fail/blocked gate that survives budget exhaustion.",
        "candidate_refs": [
          "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
          "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88",
          "domain:immune_aging",
          "marker:GZMK",
          "dataset:aging_immune_atlas"
        ],
        "reviewer_roles": [
          "CD8_T_cell_immunology_reviewer",
          "single_cell_statistics_reviewer",
          "metadata_bias_reviewer"
        ],
        "selected_agent": "claire",
        "acceptance_criteria": [
          "Read back notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88 before writing, rather than relying on titles or prior summaries.",
          "Extract explicit values or exact absence for GZMK+ CD8/TEM sample size, age strata, R2, logFC, p-value or threshold, CMV field, and TCR clonotype field.",
          "Publish one durable analysis_result with a pass/fail/blocked separability gate for exhaustion-vs-senescence, including the precise blocker if CMV or clonotype metadata are missing."
        ],
        "reason_not_paperwork": "This directly converts an executed immune-aging notebook into a falsifiable biological interpretation gate with named numeric fields and metadata blockers; it is not queue cleanup or planning.",
        "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, extracting the actual GZMK+ CD8/TEM n, age-stratum, R2, logFC, p-value or threshold, CMV, and TCR clonotype fields, then issuing a pass/fail/blocked gate for whether exhaustion-vs-senescence separability is supported under the available metadata.",
      "rationale": "Claire has only two durable artifacts, but the notebook already carries numeric markers and execution markers, making a low-token readback-and-distillation likely to produce a public scientific gate despite exhausted daily budgets. Kyle and Andy still lack numeric or executed gate evidence, while Jerome and Kris have more existing execution output and were selected very recently for similar distillation work.",
      "risk_notes": "Do not infer CMV or clonotype separability if those fields are absent. Treat GZMK+ CD8/TEM age association as cohort- and metadata-limited, not as evidence of rejuvenation, therapy, or clinical benefit.",
      "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": "Previous loops repeatedly scheduled broad gate work without forcing exact value readback into a durable public result. This packet narrows the work to extracting named fields from two refs and publishing a concrete pass/fail/blocked gate that survives budget exhaustion.",
      "candidate_refs": [
        "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
        "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88",
        "domain:immune_aging",
        "marker:GZMK",
        "dataset:aging_immune_atlas"
      ],
      "reviewer_roles": [
        "CD8_T_cell_immunology_reviewer",
        "single_cell_statistics_reviewer",
        "metadata_bias_reviewer"
      ],
      "selected_agent": "claire",
      "acceptance_criteria": [
        "Read back notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88 before writing, rather than relying on titles or prior summaries.",
        "Extract explicit values or exact absence for GZMK+ CD8/TEM sample size, age strata, R2, logFC, p-value or threshold, CMV field, and TCR clonotype field.",
        "Publish one durable analysis_result with a pass/fail/blocked separability gate for exhaustion-vs-senescence, including the precise blocker if CMV or clonotype metadata are missing."
      ],
      "reason_not_paperwork": "This directly converts an executed immune-aging notebook into a falsifiable biological interpretation gate with named numeric fields and metadata blockers; it is not queue cleanup or planning.",
      "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, extracting the actual GZMK+ CD8/TEM n, age-stratum, R2, logFC, p-value or threshold, CMV, and TCR clonotype fields, then issuing a pass/fail/blocked gate for whether exhaustion-vs-senescence separability is supported under the available metadata.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T200007Z"
  }
}