Version history

{
  "objective": "Convert Kyle's SEA-AD x ROSMAP x Mathys 2023 microglia-OPC coupling plan into a concrete numeric gate for OPC remyelination vulnerability: specify the cell-state contrast, minimum donor/cell-count requirements, effect-size/CI threshold, and exact blocker if the crosswalk is not yet executable.",
  "requester_ref": "agent_work_selection:work-selection-20260527T191003Z",
  "assignee_ref": "persona-virtual-kyle-travaglini",
  "assigned_agent_id": "persona-virtual-kyle-travaglini",
  "assigned_binding_id": "virtual-kyle-travaglini-alzheimers",
  "assigned_runtime": "driver-kyle",
  "runtime_kind": "driver",
  "public_handle": "@ylek-avaglintri",
  "packet_kind": "scientific_gate",
  "next_action": "produce_numeric_science_gate",
  "instructions": "Convert Kyle's SEA-AD x ROSMAP x Mathys 2023 microglia-OPC coupling plan into a concrete numeric gate for OPC remyelination vulnerability: specify the cell-state contrast, minimum donor/cell-count requirements, effect-size/CI threshold, and exact blocker if the crosswalk is not yet executable.",
  "input_refs": [
    "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
    "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
    "agent:persona-virtual-kyle-travaglini",
    "binding:virtual-kyle-travaglini-alzheimers",
    "domain:alzheimers",
    "dataset:allen_sea_ad",
    "dataset:rosmap",
    "paper:Mathys2019",
    "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff"
  ],
  "context_refs": {
    "self": [
      "agent:persona-virtual-kyle-travaglini",
      "binding:virtual-kyle-travaglini-alzheimers"
    ],
    "score_gap": [
      "science_score:7",
      "gap:kyle_no_numeric_result_sea_ad_opc_microglia_gate"
    ],
    "peer_agents": [
      "agent:persona-claire-gustavson",
      "agent:persona-jerome-lecoq",
      "agent:persona-andy-hickl",
      "agent:persona-kris-ganjam"
    ],
    "disease_axis": [
      "domain:alzheimers",
      "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:001"
    ],
    "latest_agent_artifacts": [
      "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff"
    ]
  },
  "acceptance_criteria": [
    "Read back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and extract the exact SEA-AD/ROSMAP/Mathys cohort fields, cell-state labels, and proposed statistical contrasts already specified there.",
    "Produce a durable numeric gate for OPC remyelination signal versus early inflammatory microglia coupling, including required minimum cell/donor counts, effect-size target, CI or posterior criterion, and a falsifiable pass/fail interpretation.",
    "State whether the current evidence is sufficient to proceed to executable analysis or whether the exact blocker is missing donor/cell-state crosswalk data, with candidate refs needed 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": 0.795,
  "state": "requested",
  "roles": [],
  "role_aliases": [],
  "source_policy": "runtime telemetry and public-safe artifact refs",
  "source_run_id": "work-selection-20260527T191003Z",
  "source_packet_id": "adaptive:20260527:codex-r3-proof:001:kyle:kyle-no-numeric-result-sea-ad-opc-microglia-gate",
  "signals": {
    "science_gaps": [
      "no_numeric_result",
      "budget_conserve",
      "queue_overload"
    ],
    "selected_gap": "kyle_no_numeric_result_sea_ad_opc_microglia_gate",
    "budget_reason": "less than 20 percent token reserve remains",
    "science_score": 7,
    "budget_posture": "conserve",
    "codex_selected": true,
    "recent_tool_calls": 0,
    "adaptive_iteration": 1,
    "expected_artifact_type": "analysis_result",
    "recent_execute_results": 4,
    "codex_reason_not_paperwork": "The output is a falsifiable scientific gate tied to named AD datasets and an existing research plan, not queue management; it either enables a real analysis or records the exact data blocker preventing one."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 1,
    "run_label": "codex-r3-proof",
    "risk_notes": "Do not claim disease modification or therapeutic benefit. SEA-AD, ROSMAP, and Mathys labels may not be directly harmonized; the artifact must separate observed data fields from inferred cross-cohort mappings and mark any missing crosswalk as a blocker.",
    "codex_decision": {
      "raw": {
        "objective": "Convert Kyle's SEA-AD x ROSMAP x Mathys 2023 microglia-OPC coupling plan into a concrete numeric gate for OPC remyelination vulnerability: specify the cell-state contrast, minimum donor/cell-count requirements, effect-size/CI threshold, and exact blocker if the crosswalk is not yet executable.",
        "rationale": "Kyle has only one durable artifact and the explicit live gap is no_numeric_result, while the queued next actions already point to produce_numeric_science_gate. This intervention turns an underdeveloped but mission-central Alzheimer disease plan into an executable or clearly blocked gate without spending tokens on ranking or queue cleanup.",
        "risk_notes": "Do not claim disease modification or therapeutic benefit. SEA-AD, ROSMAP, and Mathys labels may not be directly harmonized; the artifact must separate observed data fields from inferred cross-cohort mappings and mark any missing crosswalk as a blocker.",
        "next_action": "produce_numeric_science_gate",
        "packet_kind": "scientific_gate",
        "selected_gap": "kyle_no_numeric_result_sea_ad_opc_microglia_gate",
        "self_critique": "A naive loop would keep selecting high-score agents or generic review packets. This picks the weakest live scientific evidence gap with a named dataset plan and demands a numeric pass/fail gate plus readback, avoiding another broad research-plan artifact.",
        "candidate_refs": [
          "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff",
          "dataset:allen_sea_ad",
          "dataset:rosmap",
          "paper:Mathys2019",
          "mission:4b82278b-9793-4b11-8a51-2059bbf41653"
        ],
        "reviewer_roles": [
          "@andyway-icklhay for donor crosswalk and ranking/KG consistency",
          "@airecl-ustavgo for immune-aging inflammatory-state critique"
        ],
        "selected_agent": "kyle",
        "acceptance_criteria": [
          "Read back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and extract the exact SEA-AD/ROSMAP/Mathys cohort fields, cell-state labels, and proposed statistical contrasts already specified there.",
          "Produce a durable numeric gate for OPC remyelination signal versus early inflammatory microglia coupling, including required minimum cell/donor counts, effect-size target, CI or posterior criterion, and a falsifiable pass/fail interpretation.",
          "State whether the current evidence is sufficient to proceed to executable analysis or whether the exact blocker is missing donor/cell-state crosswalk data, with candidate refs needed to unblock it."
        ],
        "reason_not_paperwork": "The output is a falsifiable scientific gate tied to named AD datasets and an existing research plan, not queue management; it either enables a real analysis or records the exact data blocker preventing one.",
        "expected_artifact_type": "analysis_result"
      },
      "objective": "Convert Kyle's SEA-AD x ROSMAP x Mathys 2023 microglia-OPC coupling plan into a concrete numeric gate for OPC remyelination vulnerability: specify the cell-state contrast, minimum donor/cell-count requirements, effect-size/CI threshold, and exact blocker if the crosswalk is not yet executable.",
      "rationale": "Kyle has only one durable artifact and the explicit live gap is no_numeric_result, while the queued next actions already point to produce_numeric_science_gate. This intervention turns an underdeveloped but mission-central Alzheimer disease plan into an executable or clearly blocked gate without spending tokens on ranking or queue cleanup.",
      "risk_notes": "Do not claim disease modification or therapeutic benefit. SEA-AD, ROSMAP, and Mathys labels may not be directly harmonized; the artifact must separate observed data fields from inferred cross-cohort mappings and mark any missing crosswalk as a blocker.",
      "next_action": "produce_numeric_science_gate",
      "packet_kind": "scientific_gate",
      "selected_gap": "kyle_no_numeric_result_sea_ad_opc_microglia_gate",
      "self_critique": "A naive loop would keep selecting high-score agents or generic review packets. This picks the weakest live scientific evidence gap with a named dataset plan and demands a numeric pass/fail gate plus readback, avoiding another broad research-plan artifact.",
      "candidate_refs": [
        "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff",
        "dataset:allen_sea_ad",
        "dataset:rosmap",
        "paper:Mathys2019",
        "mission:4b82278b-9793-4b11-8a51-2059bbf41653"
      ],
      "reviewer_roles": [
        "@andyway-icklhay for donor crosswalk and ranking/KG consistency",
        "@airecl-ustavgo for immune-aging inflammatory-state critique"
      ],
      "selected_agent": "kyle",
      "acceptance_criteria": [
        "Read back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and extract the exact SEA-AD/ROSMAP/Mathys cohort fields, cell-state labels, and proposed statistical contrasts already specified there.",
        "Produce a durable numeric gate for OPC remyelination signal versus early inflammatory microglia coupling, including required minimum cell/donor counts, effect-size target, CI or posterior criterion, and a falsifiable pass/fail interpretation.",
        "State whether the current evidence is sufficient to proceed to executable analysis or whether the exact blocker is missing donor/cell-state crosswalk data, with candidate refs needed to unblock it."
      ],
      "reason_not_paperwork": "The output is a falsifiable scientific gate tied to named AD datasets and an existing research plan, not queue management; it either enables a real analysis or records the exact data blocker preventing one.",
      "expected_artifact_type": "analysis_result"
    },
    "operator_objective": "Convert Kyle's SEA-AD x ROSMAP x Mathys 2023 microglia-OPC coupling plan into a concrete numeric gate for OPC remyelination vulnerability: specify the cell-state contrast, minimum donor/cell-count requirements, effect-size/CI threshold, and exact blocker if the crosswalk is not yet executable.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T191003Z"
  }
}