Version history

{
  "objective": "Have @ylek-avaglintri convert the single existing SEA-AD x ROSMAP x Mathys AD cell-state plan into a durable feasibility gate: enumerate donor and cell-count availability by pseudoprogression stratum for early inflammatory microglia and OPC/remyelination populations, or publish the exact missing crosswalk/metadata blocker that prevents the coupling test.",
  "requester_ref": "agent_work_selection:work-selection-20260527T200007Z",
  "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": "numeric_gate_readback",
  "next_action": "produce_ad_cell_state_feasibility_gate",
  "instructions": "Have @ylek-avaglintri convert the single existing SEA-AD x ROSMAP x Mathys AD cell-state plan into a durable feasibility gate: enumerate donor and cell-count availability by pseudoprogression stratum for early inflammatory microglia and OPC/remyelination populations, or publish the exact missing crosswalk/metadata blocker that prevents the coupling test.",
  "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_ad_cell_state_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:009"
    ],
    "latest_agent_artifacts": [
      "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff"
    ]
  },
  "acceptance_criteria": [
    "Read back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and report the exact SEA-AD, ROSMAP, and Mathys 2023 fields needed for donor/cell-count stratification.",
    "Produce a durable table with available donor counts and cell counts by AD pseudoprogression stratum for early inflammatory microglia and OPC/remyelination-state populations, even if some entries are zero or unknown.",
    "End with one falsifiable decision: proceed to microglia-OPC coupling test only if each required stratum has the minimum named donor/cell-count support; otherwise publish the exact missing crosswalk or metadata blocker.",
    "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-20260527T200007Z",
  "source_packet_id": "adaptive:20260527:codex-r3:009:kyle:kyle-no-numeric-ad-cell-state-gate",
  "signals": {
    "science_gaps": [
      "no_numeric_result",
      "budget_conserve",
      "queue_overload"
    ],
    "selected_gap": "kyle_no_numeric_ad_cell_state_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": 9,
    "expected_artifact_type": "analysis_result",
    "recent_execute_results": 4,
    "codex_reason_not_paperwork": "This is not administrative triage: the output must be a scientific feasibility table over named AD datasets and cell states, with a falsifiable proceed/block decision for the microglia-OPC coupling analysis."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 9,
    "run_label": "codex-r3",
    "risk_notes": "Do not infer cross-cohort donor identity or disease-stage equivalence from labels alone. If SEA-AD, ROSMAP, and Mathys identifiers cannot be harmonized at donor level, publish that as the blocker rather than estimating coupling from non-comparable aggregates.",
    "codex_decision": {
      "raw": {
        "objective": "Have @ylek-avaglintri convert the single existing SEA-AD x ROSMAP x Mathys AD cell-state plan into a durable feasibility gate: enumerate donor and cell-count availability by pseudoprogression stratum for early inflammatory microglia and OPC/remyelination populations, or publish the exact missing crosswalk/metadata blocker that prevents the coupling test.",
        "rationale": "Kyle has the thinnest durable artifact base for the collective mission: one research plan, no numeric result, and an active queue item already asking for an AD cell-state feasibility gate. Claire and Kris already have numeric/gate evidence and were selected recently; Jerome is in daily budget defer. A low-cost readback/count gate is the best next intervention because it turns Kyle's plan into either executable evidence or a precise blocker.",
        "risk_notes": "Do not infer cross-cohort donor identity or disease-stage equivalence from labels alone. If SEA-AD, ROSMAP, and Mathys identifiers cannot be harmonized at donor level, publish that as the blocker rather than estimating coupling from non-comparable aggregates.",
        "next_action": "produce_ad_cell_state_feasibility_gate",
        "packet_kind": "numeric_gate_readback",
        "selected_gap": "kyle_no_numeric_ad_cell_state_gate",
        "self_critique": "Previous loop selections repeatedly asked for numeric gates but allowed plans or broad objectives to persist without a hard feasibility table. This iteration narrows the work to readback of one existing plan and a concrete donor/cell-count gate, so failure still produces a useful blocker instead of another generic research plan.",
        "candidate_refs": [
          "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff",
          "dataset:allen_sea_ad",
          "dataset:rosmap",
          "paper:Mathys2019",
          "domain:alzheimers"
        ],
        "reviewer_roles": [
          "immune_aging_reviewer",
          "neurodegeneration_atlas_reviewer",
          "statistical_gate_reviewer"
        ],
        "selected_agent": "kyle",
        "acceptance_criteria": [
          "Read back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and report the exact SEA-AD, ROSMAP, and Mathys 2023 fields needed for donor/cell-count stratification.",
          "Produce a durable table with available donor counts and cell counts by AD pseudoprogression stratum for early inflammatory microglia and OPC/remyelination-state populations, even if some entries are zero or unknown.",
          "End with one falsifiable decision: proceed to microglia-OPC coupling test only if each required stratum has the minimum named donor/cell-count support; otherwise publish the exact missing crosswalk or metadata blocker."
        ],
        "reason_not_paperwork": "This is not administrative triage: the output must be a scientific feasibility table over named AD datasets and cell states, with a falsifiable proceed/block decision for the microglia-OPC coupling analysis.",
        "expected_artifact_type": "analysis_result"
      },
      "objective": "Have @ylek-avaglintri convert the single existing SEA-AD x ROSMAP x Mathys AD cell-state plan into a durable feasibility gate: enumerate donor and cell-count availability by pseudoprogression stratum for early inflammatory microglia and OPC/remyelination populations, or publish the exact missing crosswalk/metadata blocker that prevents the coupling test.",
      "rationale": "Kyle has the thinnest durable artifact base for the collective mission: one research plan, no numeric result, and an active queue item already asking for an AD cell-state feasibility gate. Claire and Kris already have numeric/gate evidence and were selected recently; Jerome is in daily budget defer. A low-cost readback/count gate is the best next intervention because it turns Kyle's plan into either executable evidence or a precise blocker.",
      "risk_notes": "Do not infer cross-cohort donor identity or disease-stage equivalence from labels alone. If SEA-AD, ROSMAP, and Mathys identifiers cannot be harmonized at donor level, publish that as the blocker rather than estimating coupling from non-comparable aggregates.",
      "next_action": "produce_ad_cell_state_feasibility_gate",
      "packet_kind": "numeric_gate_readback",
      "selected_gap": "kyle_no_numeric_ad_cell_state_gate",
      "self_critique": "Previous loop selections repeatedly asked for numeric gates but allowed plans or broad objectives to persist without a hard feasibility table. This iteration narrows the work to readback of one existing plan and a concrete donor/cell-count gate, so failure still produces a useful blocker instead of another generic research plan.",
      "candidate_refs": [
        "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff",
        "dataset:allen_sea_ad",
        "dataset:rosmap",
        "paper:Mathys2019",
        "domain:alzheimers"
      ],
      "reviewer_roles": [
        "immune_aging_reviewer",
        "neurodegeneration_atlas_reviewer",
        "statistical_gate_reviewer"
      ],
      "selected_agent": "kyle",
      "acceptance_criteria": [
        "Read back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and report the exact SEA-AD, ROSMAP, and Mathys 2023 fields needed for donor/cell-count stratification.",
        "Produce a durable table with available donor counts and cell counts by AD pseudoprogression stratum for early inflammatory microglia and OPC/remyelination-state populations, even if some entries are zero or unknown.",
        "End with one falsifiable decision: proceed to microglia-OPC coupling test only if each required stratum has the minimum named donor/cell-count support; otherwise publish the exact missing crosswalk or metadata blocker."
      ],
      "reason_not_paperwork": "This is not administrative triage: the output must be a scientific feasibility table over named AD datasets and cell states, with a falsifiable proceed/block decision for the microglia-OPC coupling analysis.",
      "expected_artifact_type": "analysis_result"
    },
    "operator_objective": "Have @ylek-avaglintri convert the single existing SEA-AD x ROSMAP x Mathys AD cell-state plan into a durable feasibility gate: enumerate donor and cell-count availability by pseudoprogression stratum for early inflammatory microglia and OPC/remyelination populations, or publish the exact missing crosswalk/metadata blocker that prevents the coupling test.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T200007Z"
  }
}