{ "schema_name": "soa-table-extraction", "schema_version": "1.0", "extraction_metadata": { "extracted_at": "2026-09-27T13:08:28Z", "extractor": "Claude, PDF_TO_JSON_PROMPT single-pass", "prompt_version": "3.8.1", "source_document": { "filename": "NCT04573309_soa.pdf", "document_type": "amendment", "document_version": "Protocol Amendment 3.1 (US), ALXN1840-WD-204", "document_date": "18 Mar 2022" }, "extraction_status": "ready_for_resolution", "extraction_notes": "Text-layer PDF with vector rule lines. Grid marks verified by pdftotext -bbox column binning against the rule-line column boundaries recovered from a 200 dpi raster; arrows measured from the raster.", "model": "claude-opus-5-5" }, "table_metadata": { "table_number": 1, "table_type": "main_soa", "table_title": "Table 1: Schedule of Activities", "table_purpose": "Main study schedule from Screening through EOS/ET (Day 54+/-2), including both inpatient periods and the outpatient interval", "page_start": 14, "page_end": 16, "notes": "One printed table running over pages 14-15 with the header reprinted on page 15 (de-duplicated); footnotes a-h on page 15 and i-x on page 16; page 16 has no activity rows. One label column (L=1); data columns 2-25 (24 columns: 22 day columns, UNS, EOS/ET). Abbreviations block not emitted as annotations (no term used as a marker)." }, "schedule_properties": [ { "table_number": 1, "row_position": 1, "property_name": "Study Phase", "property_name_source": { "row_position": 1, "column_position": 1, "cell_value": "", "synthesized": true }, "structure_method": "inferred_from_layout", "property_type": "epoch", "hierarchical_level": 1, "property_comment": "Top header band: 'Screening' (Days -42 to -9 and -21), 'C-I' (check-in, Day -8), a blank merged cell over Days -7 to 40, 'UNS' (unscheduled) and 'EOS or ET'. The label column for rows 1-2 is a single merged cell reading 'Study Procedures' (the activity-column heading), so the property name is synthesised. Typed epoch because the values name study phases/visit categories spanning columns; distinguishes the UNS column (whose Days cell is empty) from the others." }, { "table_number": 1, "row_position": 2, "property_name": "Period", "property_name_source": { "row_position": 2, "column_position": 1, "cell_value": "", "synthesized": true }, "structure_method": "inferred_from_layout", "property_type": "period", "hierarchical_level": 2, "property_comment": "Second header band: 'Screening', 'C-I', 'Inpatient Period 1' (merged over Days -7 to 9), 'OP' (outpatient, Days 10-22), blank at Day 23, 'Inpatient Period 2' (merged over Days 24 to 40), blank under UNS and EOS/ET. Sub-phases of the treatment phase -> period. Label cell is part of the merged 'Study Procedures' cell, so name synthesised." }, { "table_number": 1, "row_position": 3, "property_name": "Days", "property_name_source": { "row_position": 3, "column_position": 1, "cell_value": "Days" }, "property_type": "study_day", "hierarchical_level": 3, "property_comment": "Study days / day ranges relative to first ALXN1840 dose (Day 1): -42 to -9 ... 40, blank under UNS, and 'EOS Day 54+/-2'. Printed label 'Days' -> study_day." } ], "schedule_grid": [ { "table_number": 1, "row_position": 1, "column_position": 2, "cell_value": "Screening", "is_merged_cell": true, "merged_cell_range": "2:3", "annotation_markers": "a" }, { "table_number": 1, "row_position": 1, "column_position": 3, "cell_value": "Screening", "is_merged_cell": true, "merged_cell_range": "2:3", "annotation_markers": "a" }, { "table_number": 1, "row_position": 1, "column_position": 4, "cell_value": "C-I", "annotation_markers": "b" }, { "table_number": 1, "row_position": 1, "column_position": 5, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 6, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 7, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 8, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 9, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 10, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 11, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 12, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 13, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 14, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 15, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 16, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 17, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 18, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 19, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 20, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 21, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 1, "column_position": 22, "cell_value": "", "is_merged_cell": true, "merged_cell_range": "5:23" }, { "table_number": 1, "row_position": 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"table_number": 1, "row_position": 45, "column_position": 17, "cell_value": "X" }, { "table_number": 1, "row_position": 45, "column_position": 18, "cell_value": "X" }, { "table_number": 1, "row_position": 45, "column_position": 19, "cell_value": "X" }, { "table_number": 1, "row_position": 45, "column_position": 20, "cell_value": "X" }, { "table_number": 1, "row_position": 45, "column_position": 21, "cell_value": "X" }, { "table_number": 1, "row_position": 45, "column_position": 22, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 2, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 4, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 5, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 6, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 7, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 8, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 9, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 10, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 11, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 12, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 13, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 14, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 15, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 16, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 17, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 18, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 19, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 20, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 21, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 22, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 23, "cell_value": "X" }, { "table_number": 1, "row_position": 47, "column_position": 25, "cell_value": "X" } ], "annotations": [ { "annotation_marker": "a", "annotation_type": "footnote", "annotation_text": "Within 42 days of ALXN1840 administration. Details of procedures that may be performed by sites designated as “screening sites” (only in the US) are detailed in Section 8.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 1, "column_position": 2 }, { "table_number": 1, "location_type": "schedule_cell", "row_position": 1, "column_position": 3 } ] }, { "annotation_marker": "b", "annotation_type": "footnote", "annotation_text": "Participants will be admitted to the clinical research unit (CRU) at least 10 hours prior to enrollment and initiation of copper- and molybdenum-controlled diet.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 1, "column_position": 4 } ] }, { "annotation_marker": "c", "annotation_type": "footnote", "annotation_text": "At the CRU’s discretion, participants may remain in the CRU or be readmitted on Day 22 with all procedures starting on Day 23.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 2, "column_position": 13 } ] }, { "annotation_marker": "d", "annotation_type": "footnote", "annotation_text": "Unscheduled study visits may occur at any time during the study and may include any study procedure as deemed necessary by the Investigator.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 1, "column_position": 24 } ] }, { "annotation_marker": "e", "annotation_type": "footnote", "annotation_text": "Participants are required to return to the CRU Day 54+/-2; participants will be discontinued from ALXN1840 medication by their physician at the latest by the Day 54 follow-up.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 1, "column_position": 25 } ] }, { "annotation_marker": "f", "annotation_type": "footnote", "annotation_text": "Discharge from the unit may occur after completion of all procedures on Day 9 and on Day 40 and after the Investigator has reviewed all safety assessment (including safety laboratory tests) and confirmed that the participant is appropriate for discharge.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 7 } ] }, { "annotation_marker": "g", "annotation_type": "footnote", "annotation_text": "A single outpatient visit or phone call and safety laboratory assessment should occur between Day 14 and Day 18. A phone call may take place on a different day than the blood draw within the Day 14 through Day 18 period.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 8, "column_position": 13 }, { "table_number": 1, "location_type": "schedule_cell", "row_position": 33, "column_position": 13 }, { "table_number": 1, "location_type": "schedule_cell", "row_position": 34, "column_position": 13 } ] }, { "annotation_marker": "h", "annotation_type": "footnote", "annotation_text": "If needed to confirm menopause.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 11 } ] }, { "annotation_marker": "i", "annotation_type": "footnote", "annotation_text": "Parameters include age and sex. Race and ethnicity will be collected where permitted by local regulations.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 16 } ] }, { "annotation_marker": "j", "annotation_type": "footnote", "annotation_text": "Wilson disease history will include diagnosis date, method of diagnosis, history of cirrhosis, details of any previous liver biopsies performed, and treatment received.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 17 }, { "table_number": 1, "location_type": "activity_name", "row_position": 18 } ] }, { "annotation_marker": "k", "annotation_type": "footnote", "annotation_text": "A full physical examination will be performed at Screening, at check-in for the study, and at the End of the study/Early Termination Visit. A physical examination should also be performed on any participants with ongoing adverse events prior to discharge from the unit. Otherwise, a symptom-driven physical examination may be performed at other times, at the Principal Investigator’s discretion.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 19 } ] }, { "annotation_marker": "l", "annotation_type": "footnote", "annotation_text": "Height at screening only.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 20 } ] }, { "annotation_marker": "m", "annotation_type": "footnote", "annotation_text": "While in the CRU, study intervention will be administered after an overnight fast (ie, at least 10 hours) at the same time every morning; drug is to be administered with 240 mL of water and meals should be delayed a minimum of 2 hours after dosing. As an outpatient, participants are expected to take ALXN1840 at approximately the same time daily (+/-1 hour). Participants should take the medication with a glass of water on an empty stomach; meals should be delayed a minimum of 2 hours after dosing.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 25 } ] }, { "annotation_marker": "n", "annotation_type": "footnote", "annotation_text": "During the outpatient period, participants will use SMS text messaging to confirm study intervention administration.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 28, "column_position": 13 } ] }, { "annotation_marker": "o", "annotation_type": "footnote", "annotation_text": "Blood sampling for PK/PD will occur before ALXN1840 administration and represents a predose trough. See Table 2 for PK/PD sampling on Days 1, 25, 29, and 39.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 29 } ] }, { "annotation_marker": "p", "annotation_type": "footnote", "annotation_text": "PK/PD collection will include timepoints described in the schedule of PK/PD assessment for Days 1, 25, 29, and 39 (Table 2).", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 30, "column_position": 8 }, { "table_number": 1, "location_type": "schedule_cell", "row_position": 30, "column_position": 16 }, { "table_number": 1, "location_type": "schedule_cell", "row_position": 30, "column_position": 18 }, { "table_number": 1, "location_type": "schedule_cell", "row_position": 30, "column_position": 22 } ] }, { "annotation_marker": "q", "annotation_type": "footnote", "annotation_text": "Samples for serum chemistry will be obtained following a fast of at least 8 hours at the Screening Visit and at check-in. In case of rechecks, and postdose serum chemistry, participants may not have fasted for 6 or 8 hours before the serum chemistry sample is taken.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 33 } ] }, { "annotation_marker": "r", "annotation_type": "footnote", "annotation_text": "Laboratory assessment including chemistry, hematology, and coagulation parameters should be performed on Days -8, -1, 8, 23, and 28 only.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 33, "column_position": 7 }, { "table_number": 1, "location_type": "schedule_cell", "row_position": 33, "column_position": 17 } ] }, { "annotation_marker": "s", "annotation_type": "footnote", "annotation_text": "Menstruation check is for women only; women of childbearing potential should only be enrolled after a negative serum pregnancy test result at Screening. Additional urine pregnancy testing will be standard for the protocol unless serum testing is required by site policies, local regulation, or Institutional Review Boards (IRBs)/Independent Ethics Committees (IECs) (Section 10.2). In addition to pregnancy tests detailed at the visits in the SoA, females of childbearing potential will be required to perform urine pregnancy tests at least every 4 weeks at their home or the study site throughout their time in the study.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 35 }, { "table_number": 1, "location_type": "activity_name", "row_position": 43 } ] }, { "annotation_marker": "t", "annotation_type": "footnote", "annotation_text": "A single 15 mL serum sample will be retained for evaluation in the event of an unexpected safety finding; retained samples may be destroyed after completion of the clinical study report.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 36 } ] }, { "annotation_marker": "u", "annotation_type": "footnote", "annotation_text": "Vital signs measurements and ECGs should be performed predose, unless otherwise specified. Vitals signs include body temperature, heart rate, respiratory rate, and systolic and diastolic blood pressure.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 37 } ] }, { "annotation_marker": "v", "annotation_type": "footnote", "annotation_text": "Copper- and molybdenum-controlled diet will be initiated after registration/inclusion. Participants will remain on a copper/molybdenum controlled diet throughout both the inpatient Period 1 (Day -8 to Day 9) and inpatient Period 2 (Day 23 to Day 40); during this time participants will be strongly encouraged to complete all meals. While not in the CRU, participants will be encouraged to adhere to their usual copper-controlled diet.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 41 } ] }, { "annotation_marker": "w", "annotation_type": "footnote", "annotation_text": "For each input/output balance period, 24-hour urine samples are to be collected for measurement of copper and molybdenum.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 44 } ] }, { "annotation_marker": "x", "annotation_type": "footnote", "annotation_text": "For fecal samples, each individual sample will be independently collected with record of date, time, and weight of the sample.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 45 } ] } ], "review_items": [ { "id": "D1", "severity": "medium", "location": { "page": 14, "row_positions": [ 1, 2 ] }, "call_made": "The top header band (Screening / C-I / UNS / EOS or ET) is typed as the study phase (epoch, level 1) and the second band (Inpatient Period 1 / OP / Inpatient Period 2) as sub-periods (period, level 2); both names are synthesised because the label cell only reads 'Study Procedures'.", "alternative": "Type the top band as visit categories (visit) — Screening, Check-in, Unscheduled and EOS/ET read as visit names — and keep the second band as epoch.", "report_section": "2.2" }, { "id": "D2", "severity": "high", "location": { "page": 14, "row_positions": [ 23, 24 ] }, "call_made": "The arrows after the X in 'Discontinue chelation therapy' (X at Day -4 through -1) and 'Discontinue zinc therapy' (X at Day -21) are distributed as '→' over every following column through the EOS column (8:25 and 4:25), including the UNS column, because the drawn arrowhead ends inside the EOS column.", "alternative": "Stop the arrow span at Day 40 (column 23), treating the arrowhead overshoot into UNS/EOS as drawing slack, or keep only the X and treat the arrow as 'discontinued for the rest of the study' without per-column entries.", "report_section": "2.3" }, { "id": "D3", "severity": "high", "location": { "page": 15, "row_position": 31 }, "call_made": "'PD: Plasma total and PUF-Cu, LBC, ceruloplasmin, ceruloplasmin-bound Cu' (first row on page 15) is transcribed with no marks, exactly as printed.", "alternative": "Treat it as the second half of the PK blood-sampling row split by the page break (Table 2 prints PK and PD in one cell sharing marks) and copy the PK row's marks (Days 1, 4-7, 25, 26-28, 29, 30-35, 36, 37-38, 39, 40, with footnote p at Days 1, 25, 29, 39) onto the PD row.", "report_section": "2.4" } ] }