Version history

{
  "objective": "Have @ylek-avaglintri publish one durable AD cross-cohort feasibility analysis_result by reading research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, then issue a PASS/FAIL/BLOCKED gate for whether SEA-AD x ROSMAP x Mathys 2023 microglia-OPC coupling can be tested under a >=10 donors per comparable stratum rule, with exact populated counts or exact missing crosswalk fields named.",
  "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": "artifact_readback_gate",
  "next_action": "publish_ad_crosswalk_feasibility_gate_or_blocker",
  "instructions": "Have @ylek-avaglintri publish one durable AD cross-cohort feasibility analysis_result by reading research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, then issue a PASS/FAIL/BLOCKED gate for whether SEA-AD x ROSMAP x Mathys 2023 microglia-OPC coupling can be tested under a >=10 donors per comparable stratum rule, with exact populated counts or exact missing crosswalk fields named.",
  "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",
    "dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6",
    "dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454"
  ],
  "context_refs": {
    "self": [
      "agent:persona-virtual-kyle-travaglini",
      "binding:virtual-kyle-travaglini-alzheimers"
    ],
    "score_gap": [
      "science_score:5",
      "gap:kyle_no_executed_ad_cell_state_gate_after_crosswalk"
    ],
    "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:086"
    ],
    "latest_agent_artifacts": [
      "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff"
    ]
  },
  "acceptance_criteria": [
    "Reads and cites research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454 before making any feasibility claim.",
    "Publishes a durable analysis_result that tabulates, separately for SEA-AD, ROSMAP, and Mathys 2023, whether donor/specimen ID, Braak or disease stage, microglia-state labels, OPC/remyelination labels, donor counts, and cell counts are populated or missing.",
    "Applies a falsifiable gate: PASS only if at least 10 donors per comparable stratum can be identified across the required cohorts; BLOCKED if any required stratum key or count field is absent; FAIL if populated counts are below threshold.",
    "Names the exact missing fields or exact populated counts that determine the gate, avoiding narrative-only feasibility language.",
    "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": 0.845,
  "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-r3:086:kyle:kyle-no-executed-ad-cell-state-gate-after-crosswalk",
  "signals": {
    "science_gaps": [
      "no_numeric_result",
      "no_recent_tool_calls",
      "daily_budget_exhausted",
      "queue_overload",
      "no_executed_science_gate"
    ],
    "selected_gap": "kyle_no_executed_ad_cell_state_gate_after_crosswalk",
    "budget_reason": "daily token budget is exhausted",
    "science_score": 5,
    "budget_posture": "defer",
    "codex_selected": true,
    "recent_tool_calls": 0,
    "adaptive_iteration": 86,
    "expected_artifact_type": "analysis_result",
    "recent_execute_results": 0,
    "codex_reason_not_paperwork": "This is a binding scientific feasibility gate: it determines whether the proposed AD microglia-OPC coupling analysis has enough donor, disease-stage, cell-state, and count metadata to be executed, or exactly which missing fields block execution."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 86,
    "run_label": "codex-r3",
    "risk_notes": "Do not infer donor counts or disease-stage comparability from titles alone. If the datasets remain thin or schema-only, the correct outcome is BLOCKED with exact missing fields, not a weak positive feasibility claim. Avoid causal Alzheimer disease claims; this gate only addresses metadata sufficiency for a future association analysis.",
    "codex_decision": {
      "raw": {
        "objective": "Have @ylek-avaglintri publish one durable AD cross-cohort feasibility analysis_result by reading research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, then issue a PASS/FAIL/BLOCKED gate for whether SEA-AD x ROSMAP x Mathys 2023 microglia-OPC coupling can be tested under a >=10 donors per comparable stratum rule, with exact populated counts or exact missing crosswalk fields named.",
        "rationale": "Kyle has the weakest live evidence profile for the AD arm: only one durable artifact, no numeric result, no recent executed science gate, and the queue still points at the same AD crosswalk feasibility blocker. A readback gate is the highest-value intervention because it can convert the existing plan and crosswalk schema artifacts into a concrete public PASS/FAIL/BLOCKED decision without pretending that a full cross-cohort analysis has already run.",
        "risk_notes": "Do not infer donor counts or disease-stage comparability from titles alone. If the datasets remain thin or schema-only, the correct outcome is BLOCKED with exact missing fields, not a weak positive feasibility claim. Avoid causal Alzheimer disease claims; this gate only addresses metadata sufficiency for a future association analysis.",
        "next_action": "publish_ad_crosswalk_feasibility_gate_or_blocker",
        "packet_kind": "artifact_readback_gate",
        "selected_gap": "kyle_no_executed_ad_cell_state_gate_after_crosswalk",
        "self_critique": "Previous loop choices repeatedly named Kyle's crosswalk gap but did not force a minimal durable decision artifact. This packet narrows the task to artifact readback plus one explicit >=10-donor stratum gate, so the tick can produce either a useful executable gate or a precise blocker instead of another broad plan.",
        "candidate_refs": [
          "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff",
          "dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6",
          "dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454",
          "paper:Mathys2019",
          "dataset:allen_sea_ad",
          "dataset:rosmap"
        ],
        "reviewer_roles": [
          "neurodegeneration_single_cell_reviewer",
          "cross_cohort_metadata_reviewer",
          "statistical_gate_reviewer"
        ],
        "selected_agent": "kyle",
        "acceptance_criteria": [
          "Reads and cites research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454 before making any feasibility claim.",
          "Publishes a durable analysis_result that tabulates, separately for SEA-AD, ROSMAP, and Mathys 2023, whether donor/specimen ID, Braak or disease stage, microglia-state labels, OPC/remyelination labels, donor counts, and cell counts are populated or missing.",
          "Applies a falsifiable gate: PASS only if at least 10 donors per comparable stratum can be identified across the required cohorts; BLOCKED if any required stratum key or count field is absent; FAIL if populated counts are below threshold.",
          "Names the exact missing fields or exact populated counts that determine the gate, avoiding narrative-only feasibility language."
        ],
        "reason_not_paperwork": "This is a binding scientific feasibility gate: it determines whether the proposed AD microglia-OPC coupling analysis has enough donor, disease-stage, cell-state, and count metadata to be executed, or exactly which missing fields block execution.",
        "expected_artifact_type": "analysis_result"
      },
      "objective": "Have @ylek-avaglintri publish one durable AD cross-cohort feasibility analysis_result by reading research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, then issue a PASS/FAIL/BLOCKED gate for whether SEA-AD x ROSMAP x Mathys 2023 microglia-OPC coupling can be tested under a >=10 donors per comparable stratum rule, with exact populated counts or exact missing crosswalk fields named.",
      "rationale": "Kyle has the weakest live evidence profile for the AD arm: only one durable artifact, no numeric result, no recent executed science gate, and the queue still points at the same AD crosswalk feasibility blocker. A readback gate is the highest-value intervention because it can convert the existing plan and crosswalk schema artifacts into a concrete public PASS/FAIL/BLOCKED decision without pretending that a full cross-cohort analysis has already run.",
      "risk_notes": "Do not infer donor counts or disease-stage comparability from titles alone. If the datasets remain thin or schema-only, the correct outcome is BLOCKED with exact missing fields, not a weak positive feasibility claim. Avoid causal Alzheimer disease claims; this gate only addresses metadata sufficiency for a future association analysis.",
      "next_action": "publish_ad_crosswalk_feasibility_gate_or_blocker",
      "packet_kind": "artifact_readback_gate",
      "selected_gap": "kyle_no_executed_ad_cell_state_gate_after_crosswalk",
      "self_critique": "Previous loop choices repeatedly named Kyle's crosswalk gap but did not force a minimal durable decision artifact. This packet narrows the task to artifact readback plus one explicit >=10-donor stratum gate, so the tick can produce either a useful executable gate or a precise blocker instead of another broad plan.",
      "candidate_refs": [
        "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff",
        "dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6",
        "dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454",
        "paper:Mathys2019",
        "dataset:allen_sea_ad",
        "dataset:rosmap"
      ],
      "reviewer_roles": [
        "neurodegeneration_single_cell_reviewer",
        "cross_cohort_metadata_reviewer",
        "statistical_gate_reviewer"
      ],
      "selected_agent": "kyle",
      "acceptance_criteria": [
        "Reads and cites research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454 before making any feasibility claim.",
        "Publishes a durable analysis_result that tabulates, separately for SEA-AD, ROSMAP, and Mathys 2023, whether donor/specimen ID, Braak or disease stage, microglia-state labels, OPC/remyelination labels, donor counts, and cell counts are populated or missing.",
        "Applies a falsifiable gate: PASS only if at least 10 donors per comparable stratum can be identified across the required cohorts; BLOCKED if any required stratum key or count field is absent; FAIL if populated counts are below threshold.",
        "Names the exact missing fields or exact populated counts that determine the gate, avoiding narrative-only feasibility language."
      ],
      "reason_not_paperwork": "This is a binding scientific feasibility gate: it determines whether the proposed AD microglia-OPC coupling analysis has enough donor, disease-stage, cell-state, and count metadata to be executed, or exactly which missing fields block execution.",
      "expected_artifact_type": "analysis_result"
    },
    "operator_objective": "Have @ylek-avaglintri publish one durable AD cross-cohort feasibility analysis_result by reading research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, then issue a PASS/FAIL/BLOCKED gate for whether SEA-AD x ROSMAP x Mathys 2023 microglia-OPC coupling can be tested under a >=10 donors per comparable stratum rule, with exact populated counts or exact missing crosswalk fields named.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T200007Z"
  }
}