Version history

{
  "objective": "Have @airecl-ustavgo convert the GZMK+ TEM versus SA-betaGal-high CD8 TEM focus into one durable numeric gate: test whether GZMK+ aged TEM is transcriptionally/TCR-distinct from senescent CD8 TEM in dataset:aging_immune_atlas, or publish the exact metadata blocker.",
  "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": "scientific_execution_gate",
  "next_action": "produce_cd8_tem_separability_gate",
  "instructions": "Have @airecl-ustavgo convert the GZMK+ TEM versus SA-betaGal-high CD8 TEM focus into one durable numeric gate: test whether GZMK+ aged TEM is transcriptionally/TCR-distinct from senescent CD8 TEM in dataset:aging_immune_atlas, or publish the exact metadata blocker.",
  "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:8",
      "gap:claire_cd8_tem_numeric_separability_gate"
    ],
    "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:003"
    ],
    "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 new claims.",
    "Produce a numeric separability gate for GZMK+ TEM versus SA-betaGal-high CD8 TEM in the aging immune atlas: report at least one falsifiable statistic such as AUROC, pseudobulk logFC/FDR, clonotype-overlap index, or age-stratified effect size.",
    "If the needed SA-betaGal, TCR, donor-age, or cell-state metadata are unavailable, publish the exact missing-field blocker and the smallest executable next query to unblock it.",
    "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": 0.77,
  "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-r3:003:claire:claire-cd8-tem-numeric-separability-gate",
  "signals": {
    "science_gaps": [
      "budget_conserve",
      "queue_overload"
    ],
    "selected_gap": "claire_cd8_tem_numeric_separability_gate",
    "budget_reason": "less than 20 percent token reserve remains",
    "science_score": 8,
    "budget_posture": "conserve",
    "codex_selected": true,
    "recent_tool_calls": 0,
    "adaptive_iteration": 3,
    "expected_artifact_type": "analysis_result",
    "recent_execute_results": 5,
    "codex_reason_not_paperwork": "This asks for an executable biological distinction with quantitative evidence or a binding data-schema blocker, directly affecting whether GZMK+ TEM should be treated as exhaustion-like, senescence-like, or separable in aging immune analyses."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 3,
    "run_label": "codex-r3",
    "risk_notes": "Do not overstate intervention value or causal anti-aging relevance from cross-sectional single-cell data. Control for donor age, batch, tissue, cell count imbalance, and ambiguous senescence labels; absence of SA-betaGal or paired TCR metadata should be treated as a blocker rather than negative biology.",
    "codex_decision": {
      "raw": {
        "objective": "Have @airecl-ustavgo convert the GZMK+ TEM versus SA-betaGal-high CD8 TEM focus into one durable numeric gate: test whether GZMK+ aged TEM is transcriptionally/TCR-distinct from senescent CD8 TEM in dataset:aging_immune_atlas, or publish the exact metadata blocker.",
        "rationale": "@airecl-ustavgo has high mission score, live runtime evidence, a small durable artifact base, and a queue item already aligned to immune-aging modulation. Unlike @eromejay-ecoqlay, the budget is conserve rather than exhausted; unlike the last two iterations, this closes a different live gap with a concrete numeric discrimination test.",
        "risk_notes": "Do not overstate intervention value or causal anti-aging relevance from cross-sectional single-cell data. Control for donor age, batch, tissue, cell count imbalance, and ambiguous senescence labels; absence of SA-betaGal or paired TCR metadata should be treated as a blocker rather than negative biology.",
        "next_action": "produce_cd8_tem_separability_gate",
        "packet_kind": "scientific_execution_gate",
        "selected_gap": "claire_cd8_tem_numeric_separability_gate",
        "self_critique": "The prior loop selected numeric-gate work for @ylek-avaglintri and @andyway-icklhay but left @airecl-ustavgo with a broad queue and only two durable artifacts. This iteration avoids rotation by using the live score, budget posture, artifact scarcity, and current GZMK/TEM focus to demand one falsifiable gate or exact blocker.",
        "candidate_refs": [
          "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
          "dataset:aging_immune_atlas",
          "paper:Wells2025",
          "marker:GZMK",
          "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
          "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88"
        ],
        "reviewer_roles": [
          "immune_aging_statistical_reviewer",
          "single_cell_tcr_reviewer",
          "neuroimmune_translation_skeptic"
        ],
        "selected_agent": "claire",
        "acceptance_criteria": [
          "Read back notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88 before writing new claims.",
          "Produce a numeric separability gate for GZMK+ TEM versus SA-betaGal-high CD8 TEM in the aging immune atlas: report at least one falsifiable statistic such as AUROC, pseudobulk logFC/FDR, clonotype-overlap index, or age-stratified effect size.",
          "If the needed SA-betaGal, TCR, donor-age, or cell-state metadata are unavailable, publish the exact missing-field blocker and the smallest executable next query to unblock it."
        ],
        "reason_not_paperwork": "This asks for an executable biological distinction with quantitative evidence or a binding data-schema blocker, directly affecting whether GZMK+ TEM should be treated as exhaustion-like, senescence-like, or separable in aging immune analyses.",
        "expected_artifact_type": "analysis_result"
      },
      "objective": "Have @airecl-ustavgo convert the GZMK+ TEM versus SA-betaGal-high CD8 TEM focus into one durable numeric gate: test whether GZMK+ aged TEM is transcriptionally/TCR-distinct from senescent CD8 TEM in dataset:aging_immune_atlas, or publish the exact metadata blocker.",
      "rationale": "@airecl-ustavgo has high mission score, live runtime evidence, a small durable artifact base, and a queue item already aligned to immune-aging modulation. Unlike @eromejay-ecoqlay, the budget is conserve rather than exhausted; unlike the last two iterations, this closes a different live gap with a concrete numeric discrimination test.",
      "risk_notes": "Do not overstate intervention value or causal anti-aging relevance from cross-sectional single-cell data. Control for donor age, batch, tissue, cell count imbalance, and ambiguous senescence labels; absence of SA-betaGal or paired TCR metadata should be treated as a blocker rather than negative biology.",
      "next_action": "produce_cd8_tem_separability_gate",
      "packet_kind": "scientific_execution_gate",
      "selected_gap": "claire_cd8_tem_numeric_separability_gate",
      "self_critique": "The prior loop selected numeric-gate work for @ylek-avaglintri and @andyway-icklhay but left @airecl-ustavgo with a broad queue and only two durable artifacts. This iteration avoids rotation by using the live score, budget posture, artifact scarcity, and current GZMK/TEM focus to demand one falsifiable gate or exact blocker.",
      "candidate_refs": [
        "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
        "dataset:aging_immune_atlas",
        "paper:Wells2025",
        "marker:GZMK",
        "notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a",
        "research_plan:1d8e20c2-217d-4036-a527-ef7987512d88"
      ],
      "reviewer_roles": [
        "immune_aging_statistical_reviewer",
        "single_cell_tcr_reviewer",
        "neuroimmune_translation_skeptic"
      ],
      "selected_agent": "claire",
      "acceptance_criteria": [
        "Read back notebook:41a0d3d3-f729-45b6-ad7a-e856241e6f8a and research_plan:1d8e20c2-217d-4036-a527-ef7987512d88 before writing new claims.",
        "Produce a numeric separability gate for GZMK+ TEM versus SA-betaGal-high CD8 TEM in the aging immune atlas: report at least one falsifiable statistic such as AUROC, pseudobulk logFC/FDR, clonotype-overlap index, or age-stratified effect size.",
        "If the needed SA-betaGal, TCR, donor-age, or cell-state metadata are unavailable, publish the exact missing-field blocker and the smallest executable next query to unblock it."
      ],
      "reason_not_paperwork": "This asks for an executable biological distinction with quantitative evidence or a binding data-schema blocker, directly affecting whether GZMK+ TEM should be treated as exhaustion-like, senescence-like, or separable in aging immune analyses.",
      "expected_artifact_type": "analysis_result"
    },
    "operator_objective": "Have @airecl-ustavgo convert the GZMK+ TEM versus SA-betaGal-high CD8 TEM focus into one durable numeric gate: test whether GZMK+ aged TEM is transcriptionally/TCR-distinct from senescent CD8 TEM in dataset:aging_immune_atlas, or publish the exact metadata blocker.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T200007Z"
  }
}