diff --git a/audit/24A2QUAH/audit_report.json b/audit/24A2QUAH/audit_report.json new file mode 100644 index 00000000..5f4bb688 --- /dev/null +++ b/audit/24A2QUAH/audit_report.json @@ -0,0 +1,537 @@ +{ + "paper_key": "24A2QUAH", + "mode": "high-risk", + "status": "READY", + "focus": [], + "artifact_fingerprint": { + "result_json_hash": "sha256:5eb45701b7b5d5fe500dbd39f5067933ea28bbf4dc50194de709c16450e1e8e7", + "meta_json_hash": "sha256:bd91e54be392daf3d59aad2e951e41aa6002b5d34924634192a8aa16f30064ce", + "blocks_raw_hash": "sha256:3855a49598d94809dba008d9061b3655a68bd1fb92b99553fb21f6564f43f0c2", + "structured_blocks_hash": "sha256:46450971b47d79360a1cdad4e9db77efd56e7639a5e76671b41a0ab437b0b692", + "document_structure_hash": "sha256:0e974c8b279a49c03cb02e20dcf367a66e359b90ec88943aa586e5313c5bd126", + "figure_inventory_hash": "sha256:8f14ae4598fe6ccace413115ff3d08eef8b547b20e38d25fca409030852784c4", + "table_inventory_hash": "sha256:286e9884a99ac6c9f76e2c3e9d43170c517c69288e45b9c391169bada00b2f6f", + "reader_figures_hash": "sha256:0998c7bf65de45a7699c59264fbb6ec4340548df9c5e6d9671e8d6f6cfff52c5", + "resolved_metadata_hash": "sha256:acbb72f5438c23e3843ea86f3557e41a2c93cbe3c7cd8a86569346347a460ec6", + "fulltext_hash": "sha256:e289479367c8c0be4f5f44b53856d8cfa1ca96ff1138649f61c6fcde00259183", + "block_trace_hash": "sha256:935afe72c0c229ce6250ab0e6dbdc3eb62b4f1f07c20d6fe7e2d981cf306dde2", + "annotated_pages": { + "page_001.png": "sha256:dfe5e84ddb3b3d43a48ba5666ece8480e829c0375f48baec4c932d6d968a9da2", + "page_002.png": "sha256:716311248765cefaa4fd4d3ce44da7b527dfc06957655449053ab1a2a30cf7a9", + "page_003.png": "sha256:4b3ab24c27f7015214d2a676e4fe310d8ef224401ed96eba8c2e842663c341bd", + "page_004.png": "sha256:badd20dc19a4903a9158ac42d77aac3946d3e6c7c8e179b9b16f73740cf63668", + "page_005.png": "sha256:d16f88ec952080dfcfe5b919505bc420584131674c8a266ec419d095072c0b9e", + "page_006.png": "sha256:0736a358b9146051747d8d4705a721bf26c515a90ff09defbd67a63f5154b6b5", + "page_007.png": "sha256:8c358c9ed30203b0cbed3fd3132fa9d72072ae950302889959061ae14855dd8d", + "page_008.png": "sha256:397aaf499df4ae096b17b91ee51bc22a50f90b3e7945369d1a3a45d3b461fe60", + "page_009.png": "sha256:6882fcb845ed5e6fbe4284216b004ad0453c64c1e667c7be9bff3903af720b54", + "page_010.png": "sha256:aed10f550847849231c7a09210f0b909052186f5eaf04b18c4d9d0ade81f187b", + "page_011.png": "sha256:5bd58c63f5607a898583c6a0e866800c4f2389a66270715742c0cb7edd72d9f2", + "page_012.png": "sha256:db0c5d09366869e783fc0a8a9bc5bee13d1439a6ed929babe82d8922a679f231" + } + }, + "artifact_freshness": { + "missing": [], + "mismatches": [ + "document_structure older than blocks_structured", + "figure_inventory older than blocks_structured", + "table_inventory older than blocks_structured", + "reader_figures older than figure_inventory", + "resolved_metadata older than blocks_structured" + ], + "annotated_pages_rendered": [ + "page_001.png", + "page_002.png", + "page_003.png", + "page_004.png", + "page_005.png", + "page_006.png", + "page_007.png", + "page_008.png", + "page_009.png", + "page_010.png", + "page_011.png", + "page_012.png" + ] + }, + "reviewed_pages": [ + 1, + 3, + 4, + 5, + 6, + 7, + 8, + 9 + ], + "reviewed_blocks": [ + "p1:0", + "p1:1", + "p1:2", + "p1:3", + "p1:4", + "p1:5", + "p1:6", + "p1:7", + "p1:8", + "p1:9", + "p1:10", + "p1:11", + "p1:12", + "p1:13", + "p1:14", + "p1:15", + "p1:16", + "p1:17", + "p1:18", + "p1:19", + "p3:0", + "p3:1", + "p3:2", + "p3:3", + "p3:4", + "p3:5", + "p3:6", + "p3:7", + "p3:8", + "p3:9", + "p3:10", + "p4:0", + "p4:1", + "p4:2", + "p4:3", + "p4:4", + "p4:5", + "p4:6", + "p4:7", + "p4:8", + "p4:9", + "p4:10", + "p5:0", + "p5:1", + "p5:2", + "p5:3", + "p5:4", + "p5:5", + "p5:6", + "p5:7", + "p5:8", + "p5:9", + "p5:10", + "p5:11", + "p5:12", + "p6:0", + "p6:1", + "p6:2", + "p6:3", + "p6:4", + "p6:5", + "p6:6", + "p6:7", + "p6:8", + "p6:9", + "p6:10", + "p6:11", + "p6:12", + "p7:0", + "p7:1", + "p7:2", + "p7:3", + "p7:4", + "p7:5", + "p7:6", + "p7:7", + "p7:8", + "p7:9", + "p7:10", + "p7:11", + "p8:0", + "p8:1", + "p8:2", + "p8:3", + "p8:4", + "p8:5", + "p8:6", + "p8:7", + "p8:8", + "p8:9", + "p8:10", + "p8:11", + "p8:12", + "p9:0", + "p9:1", + "p9:2", + "p9:3", + "p9:4", + "p9:5", + "p9:6", + "p9:7", + "p9:8", + "p9:9", + "p9:10", + "p9:11", + "p9:12", + "p9:13", + "p9:14", + "p9:15", + "p9:16", + "p9:17", + "p9:18", + "p9:19", + "p9:20", + "p9:21", + "p9:22", + "p9:23", + "p9:24", + "p9:25", + "p9:26", + "p9:27", + "p9:28", + "p9:29", + "p9:30", + "p9:31", + "p9:32", + "p9:33", + "p9:34", + "p9:35" + ], + "findings": [ + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:9" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:10" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:11" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:12" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:13" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:14" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:15" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:16" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:17" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:18" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:19" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:20" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:21" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:22" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:23" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:24" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:25" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:26" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:27" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:28" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "frontmatter_error", + "severity": "major", + "block_ids": [], + "truth": "page 1 should have clearer frontmatter role resolution", + "pipeline_behavior": "frontmatter page retains elevated unknown_structural density", + "root_cause_hypothesis": "frontmatter anchor or noise routing weakness", + "evidence": { + "annotated_page": "annotated_pages/page_001.png", + "artifact": "page_risk_summary.json" + } + }, + { + "category": "same_page_boundary_error", + "severity": "major", + "block_ids": [], + "truth": "body/reference/backmatter boundaries should be explainable at block level", + "pipeline_behavior": "page contains mixed body/reference/tail signals", + "root_cause_hypothesis": "same-page boundary ambiguity", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "page_risk_summary.json" + } + }, + { + "category": "render_mapping_error", + "severity": "minor", + "block_ids": [ + "p1:0", + "p1:3", + "p1:4", + "p1:5", + "p1:6", + "p1:7", + "p1:8", + "p1:9", + "p1:10", + "p1:11", + "p2:12", + "p3:2", + "p3:3", + "p3:10", + "p4:2", + "p4:10", + "p5:4", + "p5:12", + "p6:2", + "p6:12" + ], + "truth": "rendered fulltext should be traceable back to source blocks", + "pipeline_behavior": "some render-default blocks are not easily mapped into the current fulltext output", + "root_cause_hypothesis": "render omission or snippet mismatch", + "evidence": { + "annotated_page": null, + "artifact": "fulltext_block_mapping_summary.json" + } + } + ] +} \ No newline at end of file diff --git a/audit/24A2QUAH/audit_report.md b/audit/24A2QUAH/audit_report.md new file mode 100644 index 00000000..0dbe94af --- /dev/null +++ b/audit/24A2QUAH/audit_report.md @@ -0,0 +1,38 @@ +# OCR Truth Audit Report - 24A2QUAH + +- Mode: `high-risk` +- Status: `READY` +- Reviewed pages: [1, 3, 4, 5, 6, 7, 8, 9] +- Reviewed blocks: 129 + +## Findings + +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `major` `frontmatter_error`: frontmatter page retains elevated unknown_structural density +- `major` `same_page_boundary_error`: page contains mixed body/reference/tail signals +- `minor` `render_mapping_error`: some render-default blocks are not easily mapped into the current fulltext output + +## Disposition Guidance + +- Use `repair` when the finding reflects a pipeline defect worth fixing now. +- Use `residual` when the finding is real but intentionally deferred. +- Do not rewrite expected truth to make current output look correct. diff --git a/audit/24A2QUAH/audit_scope.json b/audit/24A2QUAH/audit_scope.json new file mode 100644 index 00000000..d626a769 --- /dev/null +++ b/audit/24A2QUAH/audit_scope.json @@ -0,0 +1,975 @@ +{ + "mode": "high-risk", + "selected_pages": [ + 1, + 3, + 4, + 5, + 6, + 7, + 8, + 9 + ], + "required_block_ids": [ + "p1:0", + "p1:1", + "p1:2", + "p1:3", + "p1:4", + "p1:5", + "p1:6", + "p1:7", + "p1:8", + "p1:9", + "p1:10", + "p1:11", + "p1:12", + "p1:13", + "p1:14", + "p1:15", + "p1:16", + "p1:17", + "p1:18", + "p1:19", + "p3:3", + "p3:5", + "p4:3", + "p5:2", + "p5:5", + "p6:3", + "p7:3", + "p7:5", + "p8:3", + "p8:5", + "p9:4", + "p9:9", + "p9:10", + "p9:11", + "p9:12", + "p9:13", + "p9:14", + "p9:15", + "p9:16", + "p9:17", + "p9:18", + "p9:19", + "p9:20", + "p9:21", + "p9:22", + "p9:23", + "p9:24", + "p9:25", + "p9:26", + "p9:27", + "p9:28", + "p9:29", + "p9:30", + "p9:31", + "p9:32", + "p9:33", + "p9:34" + ], + "required_blocks": [ + { + "block_id": "p1:0", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:1", + "page": 1, + "required_reason": [ + "frontmatter", + "needs_resolution" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:2", + "page": 1, + "required_reason": [ + "frontmatter", + "needs_resolution" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:3", + "page": 1, + "required_reason": [ + "frontmatter", + "needs_resolution" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + 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ID 9659412, 12 pages +https://doi.org/10.1155/2020/9659412","[97.0, 96.0, 376.0, 174.0]",noise,0.9,"[""header label""]",noise,0.9,frontmatter_main_zone,support_like,none,False,False +1,1,header_image,,"[1048.0, 1.0, 1201.0, 28.0]",unknown_structural,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,frontmatter_main_zone,support_like,empty,False,True +1,2,header_image,,"[996.0, 97.0, 1105.0, 205.0]",unknown_structural,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,frontmatter_main_zone,support_like,empty,False,True +1,3,text,Review Article,"[98.0, 270.0, 308.0, 305.0]",unknown_structural,0.3,"[""short text, uncertain role""]",unknown_structural,0.3,frontmatter_main_zone,support_like,short_fragment,False,True +1,4,doc_title,Animal Models of Osteochondral Defect for Testing Biomaterials,"[97.0, 316.0, 1103.0, 354.0]",paper_title,0.8,"[""page-1 zone title_zone: Animal Models of Osteochondral Defect for Testing Biomateria""]",paper_title,0.8,frontmatter_main_zone,support_like,none,True,True +1,5,text,"Xiangbo Meng $ ^{ID} $ $ ^{1,2} $ Reihane Ziadlou, $ ^{3} $ Sibylle Grad, $ ^{3} $ Mauro Alini, $ ^{3} $ Chunyi Wen $ ^{ID} $ $ ^{4} $ Yuxiao Lai, $ ^{2} $ Ling Qin, $ ^{2,5} $ Yanyan Zhao $ ^{ID} $ $","[166.0, 417.0, 1032.0, 477.0]",authors,0.8,"[""page-1 zone author_zone: Xiangbo Meng $ ^{ID} $ $ ^{1,2} $ Reihane Ziadlou, $ ^{3} $ ""]",authors,0.8,frontmatter_main_zone,support_like,none,True,True +1,6,text," $ ^{1} $College of Pharmaceutical Sciences, Hebei University, Baoding, China","[168.0, 493.0, 689.0, 515.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: $ ^{1} $College of Pharmaceutical Sciences, Hebei University""]",affiliation,0.8,frontmatter_main_zone,support_like,affiliation_marker,True,True +1,7,text,"Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China","[169.0, 530.0, 852.0, 554.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: Shenzhen Institutes of Advanced Technology, Chinese Academy ""]",affiliation,0.8,frontmatter_main_zone,support_like,none,True,True +1,8,text," $ ^{3} $AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos Platz, Switzerland","[170.0, 558.0, 775.0, 579.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: $ ^{3} $AO Research Institute Davos, Clavadelerstrasse 8, 72""]",affiliation,0.8,frontmatter_main_zone,support_like,affiliation_marker,True,True +1,9,text," $ ^{4} $Department of Biomedical Engineering, Faculty of Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China","[170.0, 580.0, 1076.0, 622.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: $ ^{4} $Department of Biomedical Engineering, Faculty of Eng""]",affiliation,0.8,frontmatter_main_zone,support_like,affiliation_marker,True,True +1,10,text," $ ^{5} $Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, China","[169.0, 624.0, 1075.0, 667.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: $ ^{5} $Musculoskeletal Research Laboratory, Department of O""]",affiliation,0.8,frontmatter_main_zone,support_like,affiliation_marker,True,True +1,11,text,Correspondence should be addressed to Yanyan Zhao; zhaoyany606@163.com and Xinluan Wang; xl.wang@siat.ac.cn,"[168.0, 681.0, 1039.0, 705.0]",frontmatter_support,0.78,"[""first-surviving-page support text: Correspondence should be addressed to Yanyan Zhao; zhaoyany6""]",frontmatter_support,0.78,frontmatter_main_zone,support_like,none,True,True +1,12,text,Received 21 October 2019; Accepted 7 January 2020; Published 28 January 2020,"[169.0, 721.0, 757.0, 744.0]",frontmatter_noise,0.8,"[""page-1 zone journal_furniture_zone: Received 21 October 2019; Accepted 7 January 2020; Published""]",frontmatter_noise,0.8,frontmatter_main_zone,support_like,none,False,False +1,13,text,Academic Editor: Paul W. Doetsch,"[168.0, 759.0, 433.0, 781.0]",frontmatter_noise,0.8,"[""page-1 zone journal_furniture_zone: Academic Editor: Paul W. Doetsch""]",frontmatter_noise,0.8,frontmatter_main_zone,support_like,none,False,False +1,14,text,"Copyright © 2020 Xiangbo Meng et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any me","[167.0, 798.0, 1102.0, 842.0]",frontmatter_noise,0.8,"[""page-1 zone journal_furniture_zone: Copyright \u00a9 2020 Xiangbo Meng et al. This is an open access ""]",frontmatter_noise,0.8,frontmatter_main_zone,support_like,none,False,False +1,15,abstract,"The treatment of osteochondral defects (OCD) remains a great challenge in orthopaedics. Tissue engineering holds a good promise for regeneration of OCD. In the light of tissue engineering, it is criti","[168.0, 854.0, 1103.0, 1129.0]",abstract_body,0.85,"[""abstract label from Paddle OCR""]",abstract_body,0.85,frontmatter_main_zone,support_like,none,True,True +1,16,paragraph_title,1. Introduction,"[99.0, 1208.0, 261.0, 1233.0]",section_heading,0.85,"[""paragraph_title label with numbering: 1. Introduction""]",section_heading,0.85,body_zone,heading_like,heading_numbered,True,True +1,17,text,"Osteochondral defects (OCD) are a common condition caused by severe trauma, sports injuries, or physical diseases, leading to joint pain, deformity, and dysfunction [1]. Joint injuries caused by traum","[95.0, 1253.0, 586.0, 1484.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,18,text,,"[611.0, 1206.0, 1104.0, 1435.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,frontmatter_main_zone,support_like,empty,True,True +1,19,text,The current clinical treatments for repair of OCD are only palliative rather than curative [7]. The common goal of,"[611.0, 1436.0, 1106.0, 1484.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,0,number,2,"[98.0, 86.0, 114.0, 105.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +2,1,header,Biochemistry Research International,"[801.0, 85.0, 1102.0, 108.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +2,2,text,"successful treatments is to relieve pain, repair damaged tissue, and improve joint function [8]. Current methods for treatment of cartilage lesions mainly include medical treatments (nonsteroid anti-i","[96.0, 142.0, 586.0, 603.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,3,text,"In this review, we summarize the benefits and limitations of each species for reproducing specific defects, analyze and compare the similarities between animal models and human clinical conditions, an","[95.0, 603.0, 587.0, 719.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,4,paragraph_title,2. Selection Criteria and Critical Size,"[96.0, 746.0, 484.0, 772.0]",section_heading,0.85,"[""paragraph_title label with numbering: 2. Selection Criteria and Critical Size""]",section_heading,0.85,body_zone,reference_like,reference_numeric_dot,True,True +2,5,text,"2.1. General Selection Criteria. The ideal animal model should be as close to the clinical setting as possible, have biological similarity, and be a suitable model for cartilage physiology [11, 12]. A","[96.0, 788.0, 587.0, 1228.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +2,6,text,"2.2. Critical Size of OCD. The critical size defect is defined as the smallest defect size (in diameter) the animal cannot self-repair without intervention [19]. In animal experiments, the understandi","[95.0, 1265.0, 587.0, 1499.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +2,7,text,,"[611.0, 141.0, 1104.0, 673.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +2,8,paragraph_title,3. Small Animal Models,"[613.0, 694.0, 866.0, 720.0]",section_heading,0.85,"[""paragraph_title label with numbering: 3. Small Animal Models""]",section_heading,0.85,body_zone,reference_like,reference_numeric_dot,True,True +2,9,text,"Small animal models are crucial in “proof-of-concept” studies, especially for testing biosafety. In these studies, concepts are validated and in vitro results are first translated in vivo. Small anima","[611.0, 735.0, 1103.0, 990.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,10,text,"3.1. Rats. The rat models used for OCD regeneration have several advantages, as rats are inexpensive, easy to handle and house, and clinically more relevant than mice. The skeletal maturity of rats is","[611.0, 1024.0, 1104.0, 1417.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +2,11,text,"3.1.1. Experimental Protocol of Animal Surgeries. In typical procedures, animals were anaesthetized and shaved and the","[611.0, 1449.0, 1104.0, 1498.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +2,12,aside_text,"9353, 2020, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1155/2020/9659412 by CochraneChina, Wiley Online Library on [25/02/2026]. See the Terms and Conditions (https://onlinelibrary.wile","[1162.0, 31.0, 1181.0, 1576.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +3,0,header,Biochemistry Research International,"[98.0, 86.0, 399.0, 109.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +3,1,number,3,"[1087.0, 87.0, 1101.0, 106.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +3,2,figure_title,"TABLE 1: Comparison of age, cartilage, and defect size in different species.","[319.0, 142.0, 878.0, 165.0]",table_caption,0.9,"[""table prefix matched: TABLE 1: Comparison of age, cartilage, and defect size in di""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +3,3,table,
SpeciesAge of skeletal maturityCartilage thicknessCartilage volumeCritical-sized defectCommon defect depth
Rat7 mo,"[98.0, 171.0, 1103.0, 393.0]",media_asset,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +3,4,figure_title,TABLE 2: Examples of studies using rat osteochondral defect models.,"[341.0, 432.0, 857.0, 454.0]",table_caption,0.9,"[""table prefix matched: TABLE 2: Examples of studies using rat osteochondral defect ""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +3,5,table,
AuthorsAgeDefect size (diameter $ \times $ depth)LocationEndpointMaterial tested
Lee and Im [35]12 weeks,"[99.0, 461.0, 1101.0, 704.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +3,6,text,"knee was disinfected. A medial temporal medial longitudinal incision was made to expose the synovium of the knee joint, and then the trochlear groove was further exposed after the lateral patellar lux","[96.0, 740.0, 588.0, 927.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,7,text,"3.1.2. Applications of Rat OCD Model for Testing of Osteochondral Repair Materials. Using a 12-week-old rat model, Lee and Im [35] found that SOX trio-co-transduced adipose tissue derived stem cells (","[95.0, 968.0, 588.0, 1499.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +3,8,text,,"[611.0, 741.0, 1104.0, 904.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +3,9,text,"3.2. Rabbit. The rabbit model provides a suitable small animal model for assessing the repair of OCD, as rabbits have larger joints for surgical procedures [41]. The age of skeletal maturity in rabbit","[611.0, 946.0, 1105.0, 1497.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +3,10,aside_text,"9353, 2020, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1155/2020/9659412 by CochraneChina, Wiley Online Library on [25/02/2026]. See the Terms and Conditions (https://onlinelibrary.wile","[1163.0, 32.0, 1181.0, 1577.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +4,0,number,4,"[99.0, 88.0, 115.0, 107.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +4,1,header,Biochemistry Research International,"[801.0, 86.0, 1102.0, 110.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +4,2,figure_title,TABLE 3: Examples of studies using rabbit osteochondral defect models.,"[330.0, 142.0, 868.0, 166.0]",table_caption,0.9,"[""table prefix matched: TABLE 3: Examples of studies using rabbit osteochondral defe""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +4,3,table,
AuthorsAge/ weightDefect size (diameter $ \times $ depth)LocationEndpointMaterial tested
Liao et al. [42]2-2.5 kg,"[98.0, 171.0, 1101.0, 435.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +4,4,text,"3.2.1. Experimental Protocol of Animal Surgeries. In most studies, the creation of an OCD was based on the following protocol. The rabbits were anaesthetized; then, a medial peripatellar incision was ","[95.0, 473.0, 587.0, 705.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +4,5,text,"3.2.2. Applications of Rabbit OCD Models for Testing of Osteochondral Repair Materials. Liao et al. [42] prepared a novel hybrid scaffold composed of methacrylated chondroitin sulfate (CSMA), poly(eth","[95.0, 738.0, 588.0, 1498.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +4,6,paragraph_title,4. Large Animal Models,"[612.0, 474.0, 866.0, 501.0]",section_heading,0.85,"[""paragraph_title label with numbering: 4. Large Animal Models""]",section_heading,0.85,body_zone,reference_like,reference_numeric_dot,True,True +4,7,text,"The large animals, such as goats, sheep, pigs, dogs, and horses, have the advantages of joint size and cartilage thickness and also have the most similar clinical lesions to humans [55]. Although larg","[610.0, 516.0, 1104.0, 863.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,8,text,4.1. Dog. The dog is considered to be a very friendly and loving partner over the world. The social and ethical issues associated with the use of dogs as preclinical and translational animal models ar,"[611.0, 902.0, 1104.0, 1295.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +4,9,text,4.1.1. Experimental Protocol of Animal Surgeries. Dogs were anaesthetized intravenously. The dog was fixed on the operating table in a supine position and the hair was shaved over the knee joint. The ,"[610.0, 1335.0, 1104.0, 1498.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +4,10,aside_text,"9353, 2020, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1155/2020/9659412 by CochraneChina, Wiley Online Library on [25/02/2026]. See the Terms and Conditions (https://onlinelibrary.wile","[1162.0, 30.0, 1181.0, 1576.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +5,0,header,Biochemistry Research International,"[98.0, 86.0, 399.0, 109.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +5,1,number,5,"[1087.0, 87.0, 1102.0, 107.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +5,2,image,,"[256.0, 144.0, 942.0, 356.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +5,3,figure_title,FIGURE 1: The process of the OCD regeneration in rabbits. A: the OCD were generated by electric drill in the femoral patellar groove; B: a 3.2 mm in diameter and 3.0 mm deep OCD was obtained; C: the b,"[97.0, 366.0, 1103.0, 411.0]",figure_caption,0.92,"[""figure_title label: FIGURE 1: The process of the OCD regeneration in rabbits. A:""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +5,4,figure_title,TABLE 4: Examples of studies using dog osteochondral defect models.,"[337.0, 443.0, 860.0, 465.0]",table_caption,0.9,"[""table prefix matched: TABLE 4: Examples of studies using dog osteochondral defect ""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +5,5,table,
AuthorsAgeDefect size (diameter $ \times $ depth)LocationEndpointMaterial tested
Lv and Yu [59]12 months,"[98.0, 469.0, 1100.0, 694.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +5,6,text,"concurrently and medial tibial plateau. Scaffolds were implanted, and the wound layer was sutured [59].","[96.0, 731.0, 587.0, 780.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,7,text,4.1.2. Applications of Dog OCD Models for Testing of Osteochondral Repair Materials. Lv and Yu [59] investigated the articular OCD (6 mm diameter and 12 mm depth) repair using a composite lamellar sca,"[96.0, 813.0, 588.0, 1254.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +5,8,text,"4.2. Pig. Pigs are considered to be a suitable animal model for mimicking human diseases and have widely been used in biomedical research [63, 64]. The pig joint size, weight requirements, and cartila","[95.0, 1289.0, 587.0, 1499.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +5,9,text,,"[610.0, 731.0, 1103.0, 986.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +5,10,text,"4.2.1. Experimental Protocol of Animal Surgeries. After animals were anaesthetized, a 5 cm incision was created in the skin to expose the medial condyle. A cylindrical OCD was created in the knee join","[611.0, 1021.0, 1103.0, 1186.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +5,11,text,4.2.2. Applications of Pig OCD Models for Testing of Osteochondral Repair Materials. Several studies on cartilage and cartilage defects have been reported using min-pig. Christensen and coauthors [68],"[610.0, 1219.0, 1105.0, 1498.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +5,12,aside_text,"9353, 2020, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1155/2020/9659412 by CochraneChina, Wiley Online Library on [25/02/2026]. See the Terms and Conditions (https://onlinelibrary.wile","[1163.0, 31.0, 1181.0, 1576.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +6,0,number,6,"[99.0, 88.0, 115.0, 107.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +6,1,header,Biochemistry Research International,"[801.0, 86.0, 1102.0, 110.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +6,2,figure_title,TABLE 5: Examples of studies using pig osteochondral defect models.,"[340.0, 142.0, 857.0, 166.0]",table_caption,0.9,"[""table prefix matched: TABLE 5: Examples of studies using pig osteochondral defect ""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +6,3,table,
AuthorsAgeDefect size (diameter $ \times $ depth)LocationEndpointMaterial tested
Christensen et al. [68]19.8 mont,"[98.0, 172.0, 1101.0, 371.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +6,4,text,enhance the mechanical properties and histological appearance of cartilage regenerates in mini-pig OCD models.,"[95.0, 404.0, 586.0, 453.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,5,text,"4.3. Sheep. Sheep is one of the commonly used animal models in orthopaedic research. The anatomy of the knee is similar to humans. However, due to the thinness of the cartilage, most of the defects ar","[96.0, 485.0, 587.0, 877.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +6,6,text,"4.3.1. Experimental Protocol of Animal Surgeries. The sheep were anaesthetized; then, sheep were placed in dorsal recumbency. The skin on the right knee was sterilized and was ready for sterile surger","[95.0, 909.0, 587.0, 1120.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +6,7,text,4.3.2. Applications of Sheep OCD Models for Testing of Osteochondral Repair Materials. Schlichting et al. [70] created an 8 mm in diameter and 15 mm deep OCD in the femoral condyles of 24 sheep to pro,"[95.0, 1150.0, 588.0, 1499.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +6,8,text,,"[611.0, 402.0, 1104.0, 569.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +6,9,text,"4.4. Goat. Goats are similar to sheep and are easy to raise and manage. The skeletal maturity of goats is similar to that of sheep, namely, about 2 to 3 years [11]. Goats aged between 2 and 4 years ha","[611.0, 600.0, 1104.0, 1061.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +6,10,text,"4.4.1. Experimental Protocol of Animal Surgeries. Surgery was performed under general anesthesia via joint surgery. Using retractors with the limb placed at maximal flexion, the implantation site was ","[611.0, 1093.0, 1104.0, 1278.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +6,11,text,4.4.2. Applications of Goat OCD Models for Testing of Osteochondral Repair Materials. Goat has been successfully used as a model for OCD to evaluate new implants. Zhang et al. [76] fabricated BMSC-int,"[611.0, 1309.0, 1105.0, 1499.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +6,12,aside_text,"9353, 2020, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1155/2020/9659412 by CochraneChina, Wiley Online Library on [25/02/2026]. See the Terms and Conditions (https://onlinelibrary.wile","[1162.0, 31.0, 1182.0, 1576.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +7,0,header,Biochemistry Research International,"[98.0, 86.0, 400.0, 110.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +7,1,number,7,"[1086.0, 86.0, 1102.0, 107.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +7,2,figure_title,TABLE 6: Examples of studies using sheep osteochondral defect models.,"[330.0, 142.0, 867.0, 166.0]",table_caption,0.9,"[""table prefix matched: TABLE 6: Examples of studies using sheep osteochondral defec""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +7,3,table,
AuthorsAgeDefect size (diameter $ \times $ depth)LocationEndpointMaterial tested
Schlichting et al. [70]2 and 3 y,"[99.0, 170.0, 1099.0, 413.0]",media_asset,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +7,4,figure_title,TABLE 7: Examples of studies using goat osteochondral defect models.,"[336.0, 452.0, 863.0, 476.0]",table_caption,0.9,"[""table prefix matched: TABLE 7: Examples of studies using goat osteochondral defect""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +7,5,table,
AuthorsAge/ weightDefect size (diameter $ \times $ depth)LocationEndpointMaterial tested
Zhang et al. [76]12 mont,"[97.0, 482.0, 1100.0, 743.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +7,6,text,found that PRP would further enhance the regenerative capacity of DBM. Kon et al. [78] created critical-sized defects of 6 mm diameter and 10 mm depth in the medial femoral condyle of the knee joint. ,"[95.0, 782.0, 588.0, 1130.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,7,text,"4.5. Horse. As horses are robust and long-lived animals, they are suitable models for assessing the repair of superficial cartilage and subchondral bone in chronic injuries in weight-bearing condition","[95.0, 1174.0, 588.0, 1499.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +7,8,text,,"[611.0, 781.0, 1104.0, 1015.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +7,9,text,4.5.1. Experimental Protocol of Animal Surgeries. Horse was positioned in dorsal recumbence. General anesthesia was maintained and a 5 cm incision made between the middle and medial patellar ligaments,"[611.0, 1047.0, 1104.0, 1278.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +7,10,text,4.5.2. Applications of Horse OCD Models for Testing of Osteochondral Repair Materials. Bolanos et al. [84] used a horse model to investigate the effect of decellularized cartilage-derived matrix (CDM),"[611.0, 1310.0, 1104.0, 1499.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,heading_numbered,True,True +7,11,aside_text,"9353, 2020, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1155/2020/9659412 by CochraneChina, Wiley Online Library on [25/02/2026]. See the Terms and Conditions (https://onlinelibrary.wile","[1162.0, 31.0, 1181.0, 1577.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +8,0,number,8,"[99.0, 87.0, 115.0, 106.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +8,1,header,Biochemistry Research International,"[801.0, 86.0, 1102.0, 109.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +8,2,figure_title,TABLE 8: Examples of studies using horse osteochondral defect models.,"[331.0, 142.0, 867.0, 165.0]",table_caption,0.9,"[""table prefix matched: TABLE 8: Examples of studies using horse osteochondral defec""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +8,3,table,
AuthorsAgeDefect size (diameter $ \times $ depth)LocationEndpointMaterial tested
Seo et al. [83]3.6 $ \pm $ 2.3 ,"[98.0, 171.0, 1099.0, 394.0]",media_asset,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +8,4,figure_title,TABLE 9: Examples of studies using monkey cartilage or osteochondral defect models.,"[277.0, 438.0, 920.0, 462.0]",table_caption,0.9,"[""table prefix matched: TABLE 9: Examples of studies using monkey cartilage or osteo""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +8,5,table,
AuthorsAgeDefect size (diameter $ \times $ depth)LocationEndpointTreatment
Buckwalter et al. [90]—3.2 mm,"[98.0, 468.0, 1101.0, 649.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +8,6,text,and platelet-rich plasma (PRP) for repairing of OCD in horses. The results showed that the GT/MSCs/BMP-2/PRP implantation promoted osteochondral regeneration in the equine model. McCarrel et al. [85] ,"[95.0, 684.0, 588.0, 963.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +8,7,paragraph_title,5. Nonhuman Primate Model,"[97.0, 993.0, 406.0, 1018.0]",section_heading,0.85,"[""paragraph_title label with numbering: 5. Nonhuman Primate Model""]",section_heading,0.85,body_zone,reference_like,reference_numeric_dot,True,True +8,8,text,"Most animal models differ in biomechanical functions and/or physiological responses from human, limiting the ability to extrapolate data to clinical practice. The nonhuman primate (NHP) models overcom","[96.0, 1035.0, 588.0, 1497.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +8,9,text,,"[609.0, 685.0, 1104.0, 1054.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +8,10,paragraph_title,6. Selecting an Appropriate Animal Model Based on Multiple Factors,"[612.0, 1083.0, 1052.0, 1136.0]",section_heading,0.85,"[""paragraph_title label with numbering: 6. Selecting an Appropriate Animal Model Based on Multiple F""]",section_heading,0.85,body_zone,reference_like,reference_numeric_dot,True,True +8,11,text,"The selection of animal models is critical to promote translational research to the clinical application of biomaterials. Generally, small animal models including rats and rabbits are beneficial for e","[609.0, 1151.0, 1105.0, 1500.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +8,12,aside_text,"9353, 2020, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1155/2020/9659412 by CochraneChina, Wiley Online Library on [25/02/2026]. See the Terms and Conditions (https://onlinelibrary.wile","[1162.0, 31.0, 1181.0, 1576.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +9,0,header,Biochemistry Research International,"[99.0, 86.0, 398.0, 109.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +9,1,number,9,"[1087.0, 88.0, 1101.0, 105.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +9,2,text,"should be considered for selecting the appropriate animal models to achieve specific study objectives, such as the size and location of the defect, age, study duration, and surgical considerations. Be","[97.0, 143.0, 586.0, 283.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,3,paragraph_title,7. Conclusion,"[98.0, 304.0, 244.0, 328.0]",section_heading,0.85,"[""paragraph_title label with numbering: 7. Conclusion""]",section_heading,0.85,body_zone,heading_like,heading_numbered,True,True +9,4,text,"In this review, we summarize the benefits and limitations of each species for reproducing specific defects, analyze and compare the similarities between animal models and human clinical situations, an","[96.0, 345.0, 586.0, 531.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,5,paragraph_title,Conflicts of Interest,"[98.0, 552.0, 312.0, 576.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Conflicts of Interest""]",subsection_heading,0.6,body_zone,heading_like,none,True,True +9,6,text,The authors declare that they have no conflicts of interest.,"[97.0, 593.0, 583.0, 617.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,7,paragraph_title,Acknowledgments,"[98.0, 639.0, 292.0, 664.0]",sub_subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level sub_subsection_heading: Acknowledgments""]",sub_subsection_heading,0.6,body_zone,heading_like,short_fragment,True,True +9,8,text,"This work was supported by the National Natural Science Foundation of China (81773964), Sino-Swiss collaborative project from Ministry of Science and Technology (2015DFG32200), the Swiss National Scie","[96.0, 681.0, 587.0, 887.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,9,paragraph_title,References,"[99.0, 909.0, 216.0, 934.0]",reference_heading,0.9,"[""references heading: References""]",reference_heading,0.9,reference_zone,heading_like,short_fragment,True,True +9,10,reference_content,"[1] C. Deng, J. Chang, and C. Wu, “Bioactive scaffolds for osteochondral regeneration,” Journal of Orthopaedic Translation, vol. 17, pp. 15–25, 2019.","[110.0, 951.0, 584.0, 1013.0]",reference_item,0.85,"[""reference content label: [1] C. Deng, J. Chang, and C. Wu, \u201cBioactive scaffolds for o""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +9,11,reference_content,"[2] W. Yuk-wai Lee and B. Wang, ""Cartilage repair by mesenchymal stem cells: clinical trial update and perspectives,"" Journal of Orthopaedic Translation, vol. 9, pp. 76–88, 2017.","[111.0, 1015.0, 584.0, 1077.0]",reference_item,0.85,"[""reference content label: [2] W. Yuk-wai Lee and B. Wang, \""Cartilage repair by mesench""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +9,12,reference_content,"[3] T. Vos, A. D. Flaxman, M. Naghavi, and R. Lozano, “Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990–2010: a systematic analysis for the global burden of disea","[110.0, 1078.0, 584.0, 1180.0]",reference_item,0.85,"[""reference content label: [3] T. Vos, A. D. Flaxman, M. Naghavi, and R. Lozano, \u201cYears""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +9,13,reference_content,"[4] D. Pereira, B. Peleteiro, J. Araújo, J. Branco, R. A. Santos, and E. Ramos, “The effect of osteoarthritis definition on prevalence and incidence estimates: a systematic review,” Osteoarthritis and","[110.0, 1183.0, 584.0, 1265.0]",reference_item,0.85,"[""reference content label: [4] D. Pereira, B. Peleteiro, J. Ara\u00fajo, J. Branco, R. A. Sa""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +9,14,reference_content,"[5] C. Deng, H. Zhu, J. 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Di Giancamillo et al., “Animal models for cartilage repair,” Journal of Biological Regulators and Homeostatic Agents, vol. 32, no. 6 Suppl. 1, pp. 105–116, 2018.","[101.0, 1045.0, 586.0, 1125.0]",reference_item,0.85,"[""reference content label: [94] I. Tessaro, V. T. Nguyen, A. Di Giancamillo et al., \u201cAn""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +12,14,aside_text,"9353, 2020, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1155/2020/9659412 by CochraneChina, Wiley Online Library on [25/02/2026]. 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AuthorsAgeDefect size (diameter $ \\times $ dept", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p8:4", + "page": 8, + "role": "table_caption", + "zone": "display_zone", + "render_default": true, + "snippet": "TABLE 9: Examples of studies using monkey cartilage or osteochondral defect mode", + "found_in_fulltext": true, + "fulltext_offset": 29535 + }, + { + "block_id": "p8:6", + "page": 8, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "and platelet-rich plasma (PRP) for repairing of OCD in horses. The results showe", + "found_in_fulltext": true, + "fulltext_offset": 29619 + }, + { + "block_id": "p8:7", + "page": 8, + "role": "section_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "5. Nonhuman Primate Model", + "found_in_fulltext": true, + "fulltext_offset": 30277 + }, + { + "block_id": "p8:8", + "page": 8, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Most animal models differ in biomechanical functions and/or physiological respon", + "found_in_fulltext": true, + "fulltext_offset": 30303 + }, + { + "block_id": "p8:10", + "page": 8, + "role": "section_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "6. Selecting an Appropriate Animal Model Based on Multiple Factors", + "found_in_fulltext": true, + "fulltext_offset": 32324 + }, + { + "block_id": "p8:11", + "page": 8, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The selection of animal models is critical to promote translational research to ", + "found_in_fulltext": true, + "fulltext_offset": 32391 + }, + { + "block_id": "p8:12", + "page": 8, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "9353, 2020, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1155/2020/", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p9:0", + "page": 9, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "Biochemistry Research International", + "found_in_fulltext": true, + "fulltext_offset": 239 + }, + { + "block_id": "p9:1", + "page": 9, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "9", + "found_in_fulltext": true, + "fulltext_offset": 316 + }, + { + "block_id": "p9:2", + "page": 9, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "should be considered for selecting the appropriate animal models to achieve spec", + "found_in_fulltext": true, + "fulltext_offset": 33297 + }, + { + "block_id": "p9:3", + "page": 9, + "role": "section_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "7. Conclusion", + "found_in_fulltext": true, + "fulltext_offset": 33616 + }, + { + "block_id": "p9:4", + "page": 9, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "In this review, we summarize the benefits and limitations of each species for re", + "found_in_fulltext": true, + "fulltext_offset": 4345 + }, + { + "block_id": "p9:5", + "page": 9, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "Conflicts of Interest", + "found_in_fulltext": true, + "fulltext_offset": 34055 + }, + { + "block_id": "p9:6", + "page": 9, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The authors declare that they have no conflicts of interest.", + "found_in_fulltext": true, + "fulltext_offset": 34077 + }, + { + "block_id": "p9:7", + "page": 9, + "role": "sub_subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "Acknowledgments", + "found_in_fulltext": true, + "fulltext_offset": 34141 + }, + { + "block_id": "p9:8", + "page": 9, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "This work was supported by the National Natural Science Foundation of China (817", + "found_in_fulltext": true, + "fulltext_offset": 34157 + }, + { + "block_id": "p9:9", + "page": 9, + "role": "reference_heading", + "zone": "reference_zone", + "render_default": true, + "snippet": "References", + "found_in_fulltext": true, + "fulltext_offset": 34605 + }, + { + "block_id": "p9:10", + "page": 9, + "role": "reference_item", + "zone": "reference_zone", + "render_default": true, + "snippet": "[1] C. 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"reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p16:14" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_016.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:0" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:1" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:2" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:3" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:4" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:5" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:6" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:7" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:8" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:9" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:10" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:11" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:12" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:13" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:14" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:15" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:16" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p17:17" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_017.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "same_page_boundary_error", + "severity": "major", + "block_ids": [], + "truth": "body/reference/backmatter boundaries should be explainable at block level", + "pipeline_behavior": "page contains mixed body/reference/tail signals", + "root_cause_hypothesis": "same-page boundary ambiguity", + "evidence": { + "annotated_page": "annotated_pages/page_016.png", + "artifact": "page_risk_summary.json" + } + }, + { + "category": "same_page_boundary_error", + "severity": "major", + "block_ids": [], + "truth": "body/reference/backmatter boundaries should be explainable at block level", + "pipeline_behavior": "page contains mixed body/reference/tail signals", + "root_cause_hypothesis": "same-page boundary ambiguity", + "evidence": { + "annotated_page": "annotated_pages/page_020.png", + "artifact": "page_risk_summary.json" + } + }, + { + "category": "render_mapping_error", + "severity": "minor", + "block_ids": [ + "p1:0", + "p1:1", + "p1:2", + "p1:8", + "p1:9", + "p1:10", + "p1:11", + "p2:0", + "p2:1", + "p2:3", + "p2:4", + "p2:7", + "p2:8", + "p2:10", + "p3:0", + "p3:1", + "p4:1", + "p4:2", + "p5:1", + "p5:3" + ], + "truth": "rendered fulltext should be traceable back to source blocks", + "pipeline_behavior": "some render-default blocks are not easily mapped into the current fulltext output", + "root_cause_hypothesis": "render omission or snippet mismatch", + "evidence": { + "annotated_page": null, + "artifact": "fulltext_block_mapping_summary.json" + } + } + ] +} \ No newline at end of file diff --git a/audit/37LK5T97/audit_report.md b/audit/37LK5T97/audit_report.md new file mode 100644 index 00000000..bfa1b816 --- /dev/null +++ b/audit/37LK5T97/audit_report.md @@ -0,0 +1,38 @@ +# OCR Truth Audit Report - 37LK5T97 + +- Mode: `high-risk` +- Status: `READY` +- Reviewed pages: [1, 2, 3, 5, 6, 7, 8, 9, 12, 16, 20] +- Reviewed blocks: 109 + +## Findings + +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `major` `same_page_boundary_error`: page contains mixed body/reference/tail signals +- `major` `same_page_boundary_error`: page contains mixed body/reference/tail signals +- `minor` `render_mapping_error`: some render-default blocks are not easily mapped into the current fulltext output + +## Disposition Guidance + +- Use `repair` when the finding reflects a pipeline defect worth fixing now. +- Use `residual` when the finding is real but intentionally deferred. +- Do not rewrite expected truth to make current output look correct. diff --git a/audit/37LK5T97/audit_scope.json b/audit/37LK5T97/audit_scope.json new file mode 100644 index 00000000..4a01140d --- /dev/null +++ b/audit/37LK5T97/audit_scope.json @@ -0,0 +1,850 @@ +{ + "mode": "high-risk", + "selected_pages": [ + 1, + 2, + 3, + 5, + 6, + 7, + 8, + 9, + 12, + 16, + 20 + ], + "required_block_ids": [ + "p1:0", + "p1:1", + "p1:2", + "p1:3", + "p1:4", + "p1:5", + "p1:6", + "p1:7", + "p1:8", + "p1:9", + "p1:10", + "p1:11", + "p1:12", + "p2:3", + "p2:9", + "p3:9", + "p5:1", + "p6:1", + "p7:1", + "p8:1", + "p9:1", + "p12:3", + "p12:10", + "p16:5", + "p16:13", + "p16:14", + "p20:2", + "p20:3", + "p20:4", + "p20:5", + "p20:6", + "p20:7", + "p20:8", + "p20:9", + "p20:10", + "p20:11", + "p20:12", + "p20:13", + "p20:14", + "p20:15", + "p20:16", + "p20:17", + "p20:18", + "p20:19", + "p20:20", + "p20:21", + "p20:22", + "p20:23" + ], + "required_blocks": [ + { + "block_id": 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Vivo,"[116.0, 208.0, 1101.0, 331.0]",paper_title,0.8,"[""page-1 zone title_zone: Endochondral Ossification for Enhancing Bone Regeneration: C""]",paper_title,0.8,frontmatter_main_zone,support_like,none,True,True +1,2,text,"S. Connor Dennis, BS, $ ^{1,2} $ Cory J. Berkland, PhD, $ ^{1-3} $ Lynda F. Bonewald, PhD, $ ^{4} $ and Michael S. Detamore, PhD $ ^{1,2} $","[334.0, 382.0, 883.0, 436.0]",authors,0.8,"[""page-1 zone author_zone: S. Connor Dennis, BS, $ ^{1,2} $ Cory J. Berkland, PhD, $ ^{""]",authors,0.8,frontmatter_main_zone,support_like,none,True,True +1,3,abstract,"Autologous bone grafting (ABG) remains entrenched as the gold standard of treatment in bone regenerative surgery. Consequently, many marginally successful bone tissue engineering strategies have focus","[112.0, 515.0, 1106.0, 1072.0]",abstract_body,0.85,"[""abstract label from Paddle OCR""]",abstract_body,0.85,frontmatter_main_zone,support_like,none,True,True +1,4,paragraph_title,Introduction,"[114.0, 1123.0, 229.0, 1145.0]",section_heading,0.9,"[""explicit scholarly heading: Introduction""]",section_heading,0.9,body_zone,heading_like,canonical_section_name,True,True +1,5,text,THE HUMAN BODY HAS AN EXTENSIVE capacity to regenerate bone tissue after trauma. Disruption of the surrounding vasculature and bone marrow resulting from a bone fracture initially facilitates a cascad,"[111.0, 1166.0, 601.0, 1367.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,6,text,,"[613.0, 1122.0, 1105.0, 1319.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,frontmatter_main_zone,support_like,empty,True,True +1,7,text,"Clinically, however, ABG remains the gold standard of treatment due to its inherent osteoconductivity, osteoinductivity,","[615.0, 1320.0, 1106.0, 1366.0]",frontmatter_noise,0.7,"[""keyword-like block: Clinically, however, ABG remains the gold standard of treatm""]",frontmatter_noise,0.7,body_zone,body_like,none,False,False +1,8,footnote," $ ^{1} $Bioengineering Program, University of Kansas, Lawrence, Kansas.","[131.0, 1400.0, 629.0, 1423.0]",footnote,0.7,"[""footnote label: $ ^{1} $Bioengineering Program, University of Kansas, Lawren""]",footnote,0.7,body_zone,body_like,affiliation_marker,True,True +1,9,footnote,"²Chemical and Petroleum Engineering Department, University of Kansas, Lawrence, Kansas.","[133.0, 1420.0, 810.0, 1439.0]",footnote,0.7,"[""footnote label: \u00b2Chemical and Petroleum Engineering Department, University o""]",footnote,0.7,body_zone,body_like,none,True,True +1,10,footnote," $ ^{3} $Pharmaceutical Chemistry Department, University of Kansas, Lawrence, Kansas.","[133.0, 1439.0, 732.0, 1458.0]",footnote,0.7,"[""footnote label: $ ^{3} $Pharmaceutical Chemistry Department, University of K""]",footnote,0.7,body_zone,body_like,affiliation_marker,True,True +1,11,footnote," $ ^{4} $Department of Oral Biology, University of Missouri-Kansas City, Kansas City, Missouri.","[133.0, 1456.0, 789.0, 1477.0]",footnote,0.7,"[""footnote label: $ ^{4} $Department of Oral Biology, University of Missouri-K""]",footnote,0.7,body_zone,body_like,affiliation_marker,True,True +1,12,number,247,"[592.0, 1500.0, 627.0, 1520.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +2,0,number,248,"[120.0, 69.0, 157.0, 88.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +2,1,header,DENNIS ET AL.,"[970.0, 68.0, 1105.0, 89.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +2,2,text,"FIG. 1. Both IM and EC ossification occurs during the bone-healing process in three overlapping regeneration phases. Critical-sized bone defects favor EC ossification over direct IM ossification, prim","[118.0, 135.0, 364.0, 640.0]",body_paragraph,0.9,"[""figure caption candidate (body narrative): FIG. 1. Both IM and EC ossification occurs during the bone-h""]",figure_caption_candidate,0.9,display_zone,legend_like,figure_number,True,True +2,3,paragraph_title,Phase I: Inflammatory 1. Hematoma Week (0-1),"[379.0, 118.0, 575.0, 179.0]",unknown_structural,0.6,"[""page-1 frontmatter title guard: Phase I: Inflammatory 1. Hematoma Week (0-1)""]",paper_title,0.6,body_zone,unknown_like,none,False,True +2,4,text,Damaged vasculature and marrow facilitate hematoma formation along with influx of inflammatory cells and BMSCs. Initial progenitor cells likely fail to survive early inflammatory phase. IM and EC ossi,"[394.0, 186.0, 553.0, 292.0]",non_body_insert,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,False,False +2,5,text,,"[586.0, 186.0, 741.0, 305.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,unknown_like,empty,True,True +2,6,text,,"[762.0, 186.0, 916.0, 305.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,unknown_like,empty,True,True +2,7,text,"Phase III: Remodeling +3. Remodeled Bone +Week ( $ \geq $ 8)","[915.0, 118.0, 1106.0, 180.0]",non_body_insert,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,False,False +2,8,text,Resorption of excess callus and replacement of woven bone with stronger lamellar bone. Dictated often by external mechanical load conditions and results in restoring healthy bone architecture.,"[931.0, 185.0, 1089.0, 305.0]",non_body_insert,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,False,False +2,9,image,,"[398.0, 306.0, 1091.0, 645.0]",media_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +2,10,text,"and thus osteogenic capabilities. $ ^{6,12-14} $ Despite these advantages, ABG has key clinical limitations, including donor site morbidity and pain, increased risk of infection, limited handling capa","[118.0, 706.0, 606.0, 1060.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,11,text,"To date, acellular biomaterial-based products have dominated the alternative bone implant market at the commercial level. $ ^{11,15,16} $ A major characteristic of these products is the ability to mim","[117.0, 1060.0, 606.0, 1388.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,12,text,"Addressing this avenue of research is the emerging paradigm of “developmental engineering” first introduced in 2009 in two reviews by Lenas et al., $ ^{22,23} $ which offer an innovative approach to e","[117.0, 1389.0, 608.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,13,text,,"[618.0, 706.0, 1109.0, 1104.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +2,14,text,"The incorporation of donor cells via SCBT strategies may provide advantageous osteo- and chondrogenic capabilities to acellular bone implants, which rely solely on recruited cells from the peripheral ","[619.0, 1103.0, 1109.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,0,header,ENDOCHONDRAL OSSIFICATION WITH NATIVE ECM AND DEVELOPMENTAL ENGINEERING,"[115.0, 67.0, 922.0, 90.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +3,1,number,249,"[1067.0, 69.0, 1103.0, 88.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +3,2,text,"in vitro cell expansion. Critical-sized bone defects often require surgical intervention within hours as opposed to weeks, because delayed bone healing leads to a higher risk of nonunion. $ ^{9} $ The","[111.0, 117.0, 602.0, 446.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,3,text,"An alternative strategy to reduce or remove the cell expansion step may reside in extending developmental engineering principles to in vivo designs (i.e., within the graft or implant), thus removing i","[111.0, 447.0, 602.0, 752.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,4,text,This review will highlight essential design criteria involved in the underexplored regenerative area of developmentally engineering bone in vivo (Fig. 2). Traditional strategies have approached tissue,"[112.0, 753.0, 602.0, 843.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,5,text,,"[614.0, 116.0, 1105.0, 492.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +3,6,paragraph_title,Overview of the Natural Bone-Healing Process,"[616.0, 522.0, 1026.0, 544.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Overview of the Natural Bone-Healing Process""]",subsection_heading,0.6,body_zone,body_like,none,True,True +3,7,text,"As mentioned earlier, the human body has an extensive capacity to regenerate bone tissue after trauma and fracture. The cellular and molecular processes involved in developmental skeletogenesis are cl","[614.0, 555.0, 1105.0, 753.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,8,text,"In general, the fracture-healing process is most often described in three overlapping phases: Inflammatory, Reparative, and Remodeling (Fig. 1), where each phase represents a complex spatiotemporal di","[614.0, 753.0, 1105.0, 843.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,9,image,,"[183.0, 881.0, 1036.0, 1333.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +3,10,figure_title,FIG. 2. Current landscape of EC ossification strategies (blue boxes) along with underexplored design space (dashed outlines) highlighted in this review. Some combined cell and material strategies are ,"[113.0, 1354.0, 1105.0, 1478.0]",figure_caption,0.92,"[""figure_title label: FIG. 2. Current landscape of EC ossification strategies (blu""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +4,0,number,250,"[120.0, 68.0, 158.0, 88.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +4,1,header,DENNIS ET AL.,"[969.0, 67.0, 1106.0, 89.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +4,2,text,"and bioactive signals. $ ^{1-9} $ Initially, disrupted vasculature and bone marrow during the inflammatory phase facilitates a coagulation cascade along with an influx of progenitor cells, including b","[117.0, 114.0, 606.0, 621.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,3,text,"In contrast, chondrogenesis predominantly occurs in avascular environments where oxygen tension is low. $ ^{39-43} $ The main consequence of this difference is that IM and EC ossification is manifeste","[117.0, 621.0, 606.0, 950.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,4,text,"While the process mentioned earlier describes successful bone regeneration within the body, it is well understood that large defects above a “critical-size” are incapable of completely restoring nativ","[117.0, 950.0, 606.0, 1239.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,5,paragraph_title,Strategies to Enhance EC Ossification Harnessing the potential of developmental engineering,"[118.0, 1255.0, 560.0, 1313.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Strategies to Enhance EC Ossification Harnessing the potenti""]",subsection_heading,0.6,body_zone,body_like,none,True,True +4,6,footer,,"[119.0, 1288.0, 560.0, 1313.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,empty,False,False +4,7,text,"Developmental engineering, a term first introduced into the tissue engineering community with two reviews in 2009 by Lenas et al., $ ^{22,23} $ involves the engineering of developmental “processes” an","[116.0, 1321.0, 606.0, 1480.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,8,text,,"[619.0, 116.0, 1108.0, 163.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +4,9,text,(1) Path dependence: successive developmental tissue relies on previous tissue formation,"[640.0, 170.0, 1108.0, 215.0]",body_paragraph,0.78,"[""default body_paragraph for text label"", ""late role resolution: non-body family 'reference_like' overrides body_paragraph"", ""style_family_authority=reference_marker"", ""context_source=block""]",body_paragraph,0.6,,reference_like,reference_numeric_parenthesis,True,True +4,10,text,(2) Robustness: tissue developmental process resistant to unintended external perturbation,"[639.0, 216.0, 1108.0, 259.0]",body_paragraph,0.78,"[""default body_paragraph for text label"", ""late role resolution: non-body family 'reference_like' overrides body_paragraph"", ""style_family_authority=reference_marker"", ""context_source=block""]",body_paragraph,0.6,,reference_like,reference_numeric_parenthesis,True,True +4,11,text,(3) Semi-autonomy: partially self-governed tissue development,"[640.0, 260.0, 1106.0, 305.0]",body_paragraph,0.78,"[""default body_paragraph for text label"", ""late role resolution: non-body family 'reference_like' overrides body_paragraph"", ""style_family_authority=reference_marker"", ""context_source=block""]",body_paragraph,0.6,,reference_like,reference_numeric_parenthesis,True,True +4,12,text,"EC ossification is a feasible route to utilize these guiding principles of developmental engineering, and the current review will cover advances made over the past decade in engineering EC ossificatio","[619.0, 313.0, 1108.0, 403.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,13,text,"While the Lenas reviews only covered replicating in vivo developmental processes in an in vitro environment, $ ^{22,23} $ the current review aims to expand their previous concept further to include re","[618.0, 404.0, 1110.0, 690.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,14,paragraph_title,Coupling in vivo developmental engineering with native ECM biomaterials,"[621.0, 718.0, 980.0, 765.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Coupling in vivo developmental engineering with native ECM b""]",subsection_heading,0.6,body_zone,body_like,none,True,True +4,15,text,Characterizing the influence of DBM on ossification pathway. Inspiration for in vivo developmental designs already exists in the form of native ECM biomaterials. There is significant evidence that EC ,"[618.0, 773.0, 1110.0, 1213.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,16,text,"Regardless of this, the DBM composition containing conductive and inductive biological agents likely influences developmental pathways during bone healing. $ ^{26-29} $ DBM composition, however, is no","[618.0, 1213.0, 1110.0, 1480.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,0,figure_title,TABLE 1. PRIMING IN VITRO CHONDROGENESIS WITH BONE MESENCHYMAL STEM CELLS FOR IN VIVO ENDOCHONDRAL OSSIFICATION,"[116.0, 225.0, 140.0, 1315.0]",table_caption,0.9,"[""table prefix matched: TABLE 1. PRIMING IN VITRO CHONDROGENESIS WITH BONE MESENCHYM""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +5,1,table,
Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Yamada et al,"[132.0, 58.0, 1070.0, 1487.0]",media_asset,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +5,2,number,251,"[592.0, 1499.0, 625.0, 1521.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +5,3,vision_footnote,(continued),"[1071.0, 69.0, 1093.0, 167.0]",footnote,0.7,"[""vision_footnote label: (continued)""]",footnote,0.7,body_zone,body_like,short_fragment,True,True +6,0,figure_title,TABLE 1. (CONTINUED),"[195.0, 669.0, 217.0, 872.0]",table_caption,0.9,"[""table prefix matched: TABLE 1. (CONTINUED)""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +6,1,table,
Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Farrell et a,"[225.0, 61.0, 1053.0, 1486.0]",media_asset,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +6,2,number,252,"[597.0, 1499.0, 631.0, 1520.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +7,0,figure_title,TABLE 1. (CONTINUED),"[174.0, 669.0, 195.0, 872.0]",table_caption,0.9,"[""table prefix matched: TABLE 1. (CONTINUED)""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +7,1,table,
Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Bahney et al,"[198.0, 68.0, 998.0, 1488.0]",media_asset,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +7,2,number,253,"[593.0, 1499.0, 626.0, 1520.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +7,3,vision_footnote,"ACs, articular chondrocytes; BMSC, bone mesenchymal stem cell; beta-TCP, beta tricalcium phosphate; EC, endochondral; GAG, glycosaminoglycan; hAC, human AC; hBMSC, human BMSC; IM, intramembranous; pBM","[975.0, 70.0, 1017.0, 1471.0]",footnote,0.7,"[""vision_footnote label: ACs, articular chondrocytes; BMSC, bone mesenchymal stem cel""]",footnote,0.7,body_zone,body_like,none,True,True +8,0,figure_title,"TABLE 2. PRIMING IN VITRO CHONDROGENESIS WITH EMBRYONIC STEM CELLS, SYNOVIUM-DERIVED STEM CELLS, ARTICULAR CHONDROCYTE AND INDICATED PITRIPOTENT STEM CELLS FOR IN VIVO ENDOCHONDRAL OSSIFICATION","[147.0, 197.0, 189.0, 1358.0]",table_caption,0.9,"[""table prefix matched: TABLE 2. PRIMING IN VITRO CHONDROGENESIS WITH EMBRYONIC STEM""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +8,1,table,
Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal modelHighlighted results
Montufar-Sol,"[176.0, 62.0, 1068.0, 1495.0]",media_asset,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +8,2,number,254,"[597.0, 1498.0, 632.0, 1521.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +8,3,vision_footnote,"ADSC, adipose-derived stem cell; ESC, embryonic stem cell; hADSC, human ADSC; hFB, human fibroblast; PBS, phosphate-buffered saline; PGA, polyglycolic acid; SVF, stromal vascular","[1037.0, 72.0, 1066.0, 1481.0]",footnote,0.7,"[""vision_footnote label: ADSC, adipose-derived stem cell; ESC, embryonic stem cell; h""]",footnote,0.7,body_zone,body_like,none,True,True +9,0,figure_title,TABLE 3. COMPARING IN VITRO CHONDROGENICALLY PRIMED CELL SOURCES FOR IN VIVO ENDOCHONDRAL OSSIFICATION,"[116.0, 276.0, 139.0, 1270.0]",table_caption,0.9,"[""table prefix matched: TABLE 3. COMPARING IN VITRO CHONDROGENICALLY PRIMED CELL SOU""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +9,1,table,
Reference(s)YearCell sourceAdditional materialsIn vitro priming methodAnimal moeaChondrogenic priming led to similar collagen type ,"[130.0, 61.0, 1127.0, 1482.0]",media_asset,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +9,2,number,255,"[592.0, 1498.0, 627.0, 1520.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +9,3,vision_footnote,"ALP, alkaline phosphatase; BCP, biphasic calcium phosphate; FPSCs, fat-pad derived stem cells; OB, osteoblast; rOB, human OB; SDSC, synovium-derived stem cell.","[1104.0, 246.0, 1128.0, 1469.0]",footnote,0.7,"[""vision_footnote label: ALP, alkaline phosphatase; BCP, biphasic calcium phosphate; ""]",footnote,0.7,body_zone,body_like,none,True,True +10,0,number,256,"[120.0, 68.0, 157.0, 89.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +10,1,header,DENNIS ET AL.,"[968.0, 67.0, 1106.0, 89.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +10,2,text,"suggesting that only implants directed toward IM ossification will possess regenerative potential. However, evidence from Rabie et al. $ ^{28,30,31} $ showed that IM and EC ossification pathways can b","[117.0, 117.0, 606.0, 534.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,3,text,"The differences in regenerative potential and developmental pathways seen in the Rabie studies were attributed to varying inductive and conductive ECM factors within DBM. $ ^{28,30-32} $ Inductive fac","[117.0, 533.0, 606.0, 1015.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,4,text,"Collectively, there is significant evidence to suggest that EC ossification can occur within native ECM biomaterials in the form of acellular DBM implants. While there has been extensive research into","[117.0, 1014.0, 606.0, 1261.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,5,text,"Exploring EC ossification potential in ECM biomaterials. In general, native ECM refers to both soluble and insoluble biomolecules that may be utilized as cell scaffolding and bioactive signaling. In a","[117.0, 1277.0, 606.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,6,text,,"[618.0, 116.0, 1108.0, 203.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +10,7,text,"Traditional bone ECM strategies: ABG intrinsically involves the grafting of native bone ECM tissue with associated autologous cells into bone defects, and it remains the gold standard of treatment in ","[618.0, 205.0, 1110.0, 774.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,8,text,"It is important to note, however, that the functional and structural properties of ECM during the bone-healing process are spatiotemporally dynamic and do not resemble healthy native bone until well i","[619.0, 774.0, 1110.0, 972.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,9,text,"Alternative ECM biomaterial strategies for EC ossification: By instead leveraging the concepts of both developmental engineering and the spatiotemporal dynamics of ECM in bone healing, there may be po","[618.0, 972.0, 1110.0, 1258.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,10,text,"Characterization of the complex cascade of signaling events and ECM changes involved in bone healing and EC ossification has been the focus of several recent reviews, $ ^{6,9,33,34} $ and readers inte","[618.0, 1256.0, 1110.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +11,0,header,ENDOCHONDRAL OSSIFICATION WITH NATIVE ECM AND DEVELOPMENTAL ENGINEERING,"[114.0, 67.0, 922.0, 90.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +11,1,number,257,"[1067.0, 69.0, 1102.0, 88.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +11,2,text,ECM biomaterials that correspond to the early and intermediate stages of native bone healing.,"[112.0, 117.0, 601.0, 162.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +11,3,text,"Native ECM biomaterials possess both conductive and inductive potential that are difficult to match with synthetic designs (e.g., non-native polymers). $ ^{17-20} $ In addition, it is increasingly evi","[111.0, 161.0, 602.0, 511.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +11,4,text,"To date, a few studies have attempted to coordinate developmental bone engineering strategies with acellular native ECM biomaterials (Figs. 1 and 2). Subsequent sections will address key features of e","[112.0, 511.0, 602.0, 666.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +11,5,text,"Inflammatory stage ECM strategies for EC ossification: Since most tissues primarily rely on broken vasculature to supply damaged areas with inflammatory signals and cells, modulating the body's initia","[111.0, 665.0, 602.0, 1038.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +11,6,text,"One strategy to enhance the regenerative response in inflammatory stage ECM strategies has been to supply the fracture space with stem cells from bone marrow aspirate, as fractured bone is supplied wi","[111.0, 1038.0, 603.0, 1481.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +11,7,text,,"[614.0, 117.0, 1105.0, 249.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +11,8,text,Coupling the evidence of low progenitor count with poor cell survival rate observed in hypoxic bone defects suggests the importance of spatiotemporal cellular recruitment strategies for bone regenerat,"[614.0, 248.0, 1105.0, 665.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +11,9,text,"Collectively, the evidence surrounding the use of inflammatory stage ECM scaffolds, signals, and recruited cells indicates that current designs remain insufficient in regenerating bone in critical-siz","[614.0, 665.0, 1105.0, 863.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +11,10,text,"Procallus stage ECM strategies for EC ossification: An intuitive source for enhancing stimulation of EC ossification is the procallus ECM, as natural bone healing progresses to this stage early in the","[614.0, 863.0, 1105.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +12,0,number,258,"[120.0, 69.0, 157.0, 88.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +12,1,header,DENNIS ET AL.,"[969.0, 67.0, 1106.0, 89.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +12,2,figure_title,TABLE 4. MODULATORS OF CHONDROCYTE HYPERTROPHY,"[373.0, 117.0, 852.0, 140.0]",table_caption,0.9,"[""table prefix matched: TABLE 4. MODULATORS OF CHONDROCYTE HYPERTROPHY""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +12,3,table,"<","[117.0, 146.0, 1104.0, 337.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +12,4,vision_footnote,"BMPs, bone morphogenic proteins; MMP, matrix metalloproteinase; TGF, transforming growth factor; IL-1β, interleukin-1β.","[135.0, 348.0, 1042.0, 371.0]",footnote,0.7,"[""vision_footnote label: BMPs, bone morphogenic proteins; MMP, matrix metalloproteina""]",footnote,0.7,body_zone,body_like,none,True,True +12,5,text,"that external chemical, $ ^{9,33,38,41,73,80-85,89,90} $ physical, $ ^{39-42} $ and mechanical cues $ ^{41,45} $ stimulated BMSCs to stay locked in a stable cartilage state or progress into a hypertro","[117.0, 399.0, 606.0, 533.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +12,6,text,"In summary, the success of in vivo developmental engineering designs for EC ossification will likely depend on the incorporation of physiologically relevant bioactive chemical mediators along with phy","[117.0, 533.0, 607.0, 843.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +12,7,paragraph_title,"Isolating, identifying, and delivering native ECM for EC ossification","[118.0, 873.0, 510.0, 918.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Isolating, identifying, and delivering native ECM for EC oss""]",subsection_heading,0.6,body_zone,body_like,none,True,True +12,8,text,Utilizing step-wise ECM strategies. Strategies to design scaffolds with incorporated native ECM components can be divided into two main categories: (1) Bottom-up approach or (2) Top-down approach (i.e,"[117.0, 929.0, 606.0, 1477.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +12,9,text,,"[618.0, 402.0, 1110.0, 713.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +12,10,image,,"[656.0, 752.0, 1076.0, 1353.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +12,11,figure_title,"FIG. 3. Top-down approaches to mimic native ECM tissue require less processing before implantation and retain more of the ECM's physicochemical composition, structure, and function compared with botto","[619.0, 1373.0, 1108.0, 1478.0]",figure_caption,0.92,"[""figure_title label: FIG. 3. Top-down approaches to mimic native ECM tissue requi""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +13,0,header,ENDOCHONDRAL OSSIFICATION WITH NATIVE ECM AND DEVELOPMENTAL ENGINEERING,"[115.0, 67.0, 923.0, 90.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +13,1,number,259,"[1067.0, 69.0, 1102.0, 88.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +13,2,text,"“raw” biomaterial re-synthesis, however, is that designs can be modular, which means that separate elements of the design can be tested independently. As a result, each component can be characterized ","[112.0, 120.0, 602.0, 751.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +13,3,text,"Step-wise designs from both allogeneic and xenogeneic tissue sources have been utilized clinically for cartilage and bone tissue engineering along with dermal, vascular, nerve, and urogenital tissue. ","[112.0, 752.0, 602.0, 1041.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +13,4,text,"Decellularized cartilage for enhancing EC ossification. Intuitively, it follows that designs mimicking the native bone or cartilage ECM hold vast potential for eliciting ossification and chondrogenesi","[112.0, 1059.0, 602.0, 1480.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +13,5,text,,"[614.0, 117.0, 1105.0, 381.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +13,6,text,"DCC, from both allogeneic and xenogeneic sources, is a poorly explored native ECM biomaterial. Recently, it has emerged as a source that is rich in both chondroinductive and chondroconductive potentia","[614.0, 381.0, 1106.0, 1171.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +13,7,text,Delivery strategies for decellularized tissues. Crucial to the future success of these ECM materials will be the strategies used to incorporate and deliver them within engineered implants. If maximum ,"[614.0, 1191.0, 1106.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +14,0,number,260,"[120.0, 69.0, 157.0, 89.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +14,1,header,DENNIS ET AL.,"[968.0, 67.0, 1106.0, 89.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +14,2,text,particle size on regenerative capacity of these materials remains unclear. A recent review of DBM clinical products and procurement by Gruskin et al. $ ^{15} $ indicated that larger particles of DBM (,"[116.0, 117.0, 606.0, 358.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +14,3,text,"While morselization strategies most often include some form of mechanical breakdown (e.g., pulverization or cyro-grinding), solubilization uses chemical and enzymatic methods (e.g., demineralization a","[116.0, 359.0, 606.0, 622.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +14,4,text,"In summary, the extent of native ECM processing required to enhance the regenerative capacity of a bone implant will be application specific. These specifications will include issues such as load-bear","[116.0, 622.0, 607.0, 931.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +14,5,paragraph_title,Incorporating SCBTs into the design,"[120.0, 961.0, 421.0, 983.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Incorporating SCBTs into the design""]",subsection_heading,0.6,body_zone,body_like,none,True,True +14,6,text,"Priming chondrogenesis in vitro for EC ossification. While acellular ECM design strategies possess great conductive and inductive potential for eliciting in vivo EC ossification, SCBTs may provide adv","[117.0, 992.0, 606.0, 1410.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +14,7,text,"The bone regeneration community has attempted to harness the advantages of SCBT strategies, either as exclusive therapies or combined and encapsulated within biomaterial implants, to overcome cell rec","[116.0, 1410.0, 606.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +14,8,text,,"[618.0, 117.0, 1109.0, 447.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +14,9,text,"Within the realm of SCBTs for bone regeneration, a majority of strategies have focused on stimulating cell populations to undergo direct osteogenesis rather than chondrogenesis. However, as previously","[618.0, 448.0, 1110.0, 1039.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +14,10,text,"While the majority of the tissue priming research aimed at establishing feasibility from a particular cell population (Tables 2 and 3), several studies compared various cell sources to elucidate diffe","[618.0, 1039.0, 1111.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,0,header,ENDOCHONDRAL OSSIFICATION WITH NATIVE ECM AND DEVELOPMENTAL ENGINEERING,"[115.0, 67.0, 922.0, 90.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,none,False,False +15,1,number,261,"[1067.0, 69.0, 1101.0, 88.0]",noise,0.9,"[""page number label""]",noise,0.9,,unknown_like,short_fragment,False,False +15,2,text,and could be a worthwhile focus of future investigation in enhancing EC ossification and bone regeneration designs.,"[113.0, 117.0, 601.0, 162.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,3,text,"Regardless of the cell source used for priming EC ossification, several generalized conclusions from the reviewed primed in vitro stem cell studies (Tables 2–4) can be summarized as follows:","[113.0, 161.0, 601.0, 251.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,4,text,(1) Chondrogenic cell priming in vitro was required to elicit EC ossification in vivo.,"[132.0, 259.0, 601.0, 302.0]",body_paragraph,0.78,"[""default body_paragraph for text label"", ""late role resolution: non-body family 'reference_like' overrides body_paragraph"", ""style_family_authority=reference_marker"", ""context_source=block""]",body_paragraph,0.6,,reference_like,reference_numeric_parenthesis,True,True +15,5,text,"(2) Cartilage templates were necessary, but not sufficient to elicit EC ossification in vivo.","[133.0, 303.0, 601.0, 346.0]",body_paragraph,0.78,"[""default body_paragraph for text label"", ""late role resolution: non-body family 'reference_like' overrides body_paragraph"", ""style_family_authority=reference_marker"", ""context_source=block""]",body_paragraph,0.6,,reference_like,reference_numeric_parenthesis,True,True +15,6,text,(a) Stable or permanent AC templates progressed through EC ossification.,"[133.0, 348.0, 600.0, 390.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +15,7,text,(3) Osteogenic priming alternatively favored IM over EC ossification.,"[133.0, 391.0, 601.0, 434.0]",body_paragraph,0.78,"[""default body_paragraph for text label"", ""late role resolution: non-body family 'reference_like' overrides body_paragraph"", ""style_family_authority=reference_marker"", ""context_source=block""]",body_paragraph,0.6,,reference_like,reference_numeric_parenthesis,True,True +15,8,text,(4) Hypertrophic chondrocyte priming elicited the most extensive EC ossification.,"[133.0, 435.0, 601.0, 479.0]",body_paragraph,0.78,"[""default body_paragraph for text label"", ""late role resolution: non-body family 'reference_like' overrides body_paragraph"", ""style_family_authority=reference_marker"", ""context_source=block""]",body_paragraph,0.6,,reference_like,reference_numeric_parenthesis,True,True +15,9,text,"While the collective evidence from these studies suggested that EC ossification remains necessarily tethered to the burden of in vitro cell priming and expansion, previous evidence was already present","[111.0, 489.0, 601.0, 688.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,10,text,"Consequently, this contradictory evidence suggests that an intermediate and underexplored strategy for bone regeneration may exist which incorporates advantages exhibited by both DBM biomaterials and ","[111.0, 688.0, 601.0, 976.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,11,text,"Intraoperative SCBT strategies with native ECM biomaterials. An emerging strategy to streamline SCBTs is to consolidate necessary cell protocols, including the harvesting, isolation, stimulation, and ","[112.0, 992.0, 602.0, 1300.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +15,12,text,"To date, however, no intraoperative SCBT approaches using either BMSCs or ADSCs derived from the stromal vascular fraction (SVF) have been able to regenerate bone in critical-sized defects without the","[112.0, 1300.0, 602.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +15,13,text,,"[614.0, 118.0, 1105.0, 489.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,,unknown_like,empty,True,True +15,14,text,"Emerging evidence in this area suggests that quick stimulation of isolated stem cells (e.g., minutes to hours) may improve differentiation and gene expression outcomes compared with untreated cells. $","[614.0, 490.0, 1105.0, 730.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +15,15,text,"Meanwhile, it should be reiterated and emphasized that native ECM biomaterials from allogeneic and xenogeneic sources possess both conductive and inductive biomolecules. $ ^{17,18,20,21} $ These bioma","[614.0, 730.0, 1104.0, 1017.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +15,16,text,"In summary, establishing the regenerative potential of acellular ECM biomaterial designs will help elucidate the additional benefits of incorporating either SCBTs or other purified inductive and condu","[614.0, 1015.0, 1105.0, 1237.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +15,17,paragraph_title,Discussion: Converging Framework of EC Ossification in the Future of Bone Regeneration,"[615.0, 1267.0, 1039.0, 1313.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Discussion: Converging Framework of EC Ossification in the F""]",subsection_heading,0.6,body_zone,unknown_like,none,True,True +15,18,text,"EC ossification, a process that naturally occurs in almost all bone-healing events, $ ^{1-9} $ can be utilized to enhance bone regeneration for nearly any orthopedic indication, especially in avascula","[614.0, 1322.0, 1105.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +16,0,number,262,"[120.0, 69.0, 157.0, 88.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +16,1,header,DENNIS ET AL.,"[969.0, 67.0, 1105.0, 89.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +16,2,text,intervention but can potentially be enhanced by combining in vivo developmental engineering strategies with biomimetic ECM biomaterials. Evidence to support this claim of utility resides in two evolvi,"[117.0, 117.0, 606.0, 402.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +16,3,text,"Currently, however, both in vitro priming and DBM strategies face formidable technical, business, and regulatory challenges that limit their feasibility as commercially competitive alternatives to the","[117.0, 402.0, 606.0, 600.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +16,4,text,"In addition, regulatory challenges exist for both strategies. $ ^{118} $ The in vitro expansion of autologous stem cells inherently involves a high level of manufacturing risk that should meet stringe","[117.0, 601.0, 606.0, 1170.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +16,5,text,"An alternative, and underexplored, developmental engineering strategy integrates the advantages of these two EC ossification approaches with a new class of ECM biomaterials that instead resemble the e","[117.0, 1169.0, 607.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,body_like,none,True,True +16,6,text,,"[618.0, 117.0, 1108.0, 270.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +16,7,text,"Although significant focus was given to acellular ECM strategies, critical perspectives on SCBTs were also discussed. While the reviewed chondrogenic priming studies collectively concluded that in vit","[619.0, 269.0, 1110.0, 930.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +16,8,text,"In summary, native ECM biomaterials inherently possessing ideal conductive, inductive, and mechanical properties have yet to be considered with regard to EC ossification and developmental engineering ","[619.0, 929.0, 1109.0, 1194.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +16,9,paragraph_title,Acknowledgments,"[622.0, 1211.0, 789.0, 1233.0]",sub_subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level sub_subsection_heading: Acknowledgments""]",sub_subsection_heading,0.6,body_zone,body_like,short_fragment,True,True +16,10,text,The authors are grateful for the support from the NIH (R01 DE022472 and R01 AR056347) and the NIGMS Predoctoral Biotechnology Training Grant Program (T32 GM-08359).,"[619.0, 1243.0, 1107.0, 1311.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +16,11,paragraph_title,Disclosure Statement,"[622.0, 1328.0, 815.0, 1350.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Disclosure Statement""]",subsection_heading,0.6,body_zone,body_like,none,True,True +16,12,text,No competing financial interests exist.,"[640.0, 1360.0, 958.0, 1384.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +16,13,paragraph_title,References,"[623.0, 1401.0, 726.0, 1423.0]",reference_heading,0.9,"[""references heading: References""]",reference_heading,0.9,reference_zone,unknown_like,short_fragment,True,True +16,14,reference_content,"1. Einhorn, T.A. The science of fracture healing. J Orthop Trauma 19, S4, 2005.","[643.0, 1434.0, 1107.0, 1475.0]",reference_item,0.85,"[""reference content label: 1. Einhorn, T.A. The science of fracture healing. J Orthop T""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +17,0,header,ENDOCHONDRAL OSSIFICATION WITH NATIVE ECM AND DEVELOPMENTAL ENGINEERING,"[116.0, 68.0, 922.0, 89.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,none,False,False +17,1,number,263,"[1067.0, 70.0, 1102.0, 88.0]",noise,0.9,"[""page number label""]",noise,0.9,,unknown_like,short_fragment,False,False +17,2,reference_content,"2. Gerstenfeld, L.C., Cullinane, D.M., Barnes, G.L., Graves, D.T., and Einhorn, T.A. Fracture healing as a post-natal developmental process: molecular, spatial, and temporal aspects of its regulation.","[134.0, 118.0, 601.0, 220.0]",reference_item,0.85,"[""reference content label: 2. Gerstenfeld, L.C., Cullinane, D.M., Barnes, G.L., Graves,""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +17,3,reference_content,"3. Kalfas, I.H. Principles of bone healing. Neurosurg Focus 10, E1, 2001.","[135.0, 223.0, 599.0, 262.0]",reference_item,0.85,"[""reference content label: 3. Kalfas, I.H. Principles of bone healing. Neurosurg Focus ""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +17,4,reference_content,"4. Meyer, U., and Weismann, H.P. Bone and cartilage. In: Schroeder, G., ed. Bone and Cartilage Engineering. New York, NY: Springer, 2006, pp. 7–46.","[134.0, 265.0, 600.0, 326.0]",reference_item,0.85,"[""reference content label: 4. Meyer, U., and Weismann, H.P. Bone and cartilage. In: Sch""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +17,5,reference_content,"5. Miclau, T., Schneider, R.A., Eames, B.F., and Helms, J.A. Common molecular mechanisms regulating fetal bone formation and adult fracture repair. In: Lieberman, J.R., and Friedlaender, G.E., eds. Bo","[136.0, 328.0, 600.0, 451.0]",reference_item,0.85,"[""reference content label: 5. Miclau, T., Schneider, R.A., Eames, B.F., and Helms, J.A.""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +17,6,reference_content,"6. Sfeir, C., Ho, L., Doll, B.A., Azari, K., and Hollinger, J.O. Fracture repair. In: Lieberman, J.R., and Friedlaender, G.E., eds. Bone Regeneration and Repair: Biology and Clinical Applications. Tot","[135.0, 453.0, 601.0, 555.0]",reference_item,0.85,"[""reference content label: 6. Sfeir, C., Ho, L., Doll, B.A., Azari, K., and Hollinger, ""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +17,7,reference_content,"7. Schindeler, A., McDonald, M.M., Bokko, P., and Little, D.G. Bone remodeling during fracture repair: the cellular picture. 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Eur Cells Mater 17, 1, 2009.","[625.0, 118.0, 1107.0, 199.0]",reference_item,0.85,"[""reference content label: 111. Tortelli, F., and Cancedda, R. Three-dimensional cultur""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +20,14,reference_content,"112. Helder, M.N., Knippenberg, M., Klein-Nulend, J., and Wuisman, P.I.J.M. Stem cells from adipose tissue allow challenging new concepts for regenerative medicine. Tissue Eng 13, 1799, 2007.","[625.0, 202.0, 1106.0, 283.0]",reference_item,0.85,"[""reference content label: 112. Helder, M.N., Knippenberg, M., Klein-Nulend, J., and Wu""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +20,15,reference_content,"113. Follmar, K.E., Prichard, H.L., DeCroos, F.C., Wang, H.T., Levin, L.S., Klitzman, B., et al. Combined bone allograft and adipose-derived stem cell autograft in a rabbit model. 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Detamore, PhD +Chemical and Petroleum Engineering Department +University of Kansas +4163 Learned Hall +1530 West 15th Street +Lawrence, KS 66045-7618","[693.0, 866.0, 1110.0, 1022.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,True,True +20,22,text,E-mail: detamore@ku.edu,"[889.0, 1025.0, 1108.0, 1047.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,True,True +20,23,text,"Received: July 14, 2014 +Accepted: October 20, 2014 +Online Publication Date: December 3, 2014","[741.0, 1057.0, 1110.0, 1124.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,True,True diff --git a/audit/37LK5T97/figure_table_ownership_summary.json b/audit/37LK5T97/figure_table_ownership_summary.json new file mode 100644 index 00000000..8f7f1b61 --- /dev/null +++ b/audit/37LK5T97/figure_table_ownership_summary.json @@ -0,0 +1,37 @@ +{ + "figures": { + "matched_count": 2, + "ambiguous_count": 0, + "unresolved_cluster_count": 0, + "unmatched_asset_count": 1, + "matched": [ + { + "figure_number": 2, + "legend_block_id": 10, + "asset_block_ids": [ + 9 + ], + "page": 3, + "match_type": null + }, + { + "figure_number": 3, + "legend_block_id": 11, + "asset_block_ids": [ + 10 + ], + "page": 12, + "match_type": null + } + ], + "ambiguous": [], + "unresolved": [] + }, + "tables": { + "matched_count": 0, + "ambiguous_count": 0, + "unmatched_asset_count": 6, + "matched": [], + "ambiguous": [] + } +} \ No newline at end of file diff --git a/audit/37LK5T97/fulltext_block_mapping_summary.json b/audit/37LK5T97/fulltext_block_mapping_summary.json new file mode 100644 index 00000000..0ca38535 --- /dev/null +++ b/audit/37LK5T97/fulltext_block_mapping_summary.json @@ -0,0 +1,2707 @@ +{ + "mappable_block_count": 270, + "found_count": 215, + "missing_count": 55, + "rows": [ + { + "block_id": "p1:0", + "page": 1, + "role": "noise", + "zone": "frontmatter_main_zone", + "render_default": false, + "snippet": "TISSUE ENGINEERING: Part B Volume 21, Number 3, 2015 © Mary Ann Liebert, Inc. 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"annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p10:9" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p10:10" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p10:11" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p10:12" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p10:13" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p10:14" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p10:15" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p10:16" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p10:17" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p10:18" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p10:19" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "same_page_boundary_error", + "severity": "major", + "block_ids": [], + "truth": "body/reference/backmatter boundaries should be explainable at block level", + "pipeline_behavior": "page contains mixed body/reference/tail signals", + "root_cause_hypothesis": "same-page boundary ambiguity", + "evidence": { + "annotated_page": "annotated_pages/page_010.png", + "artifact": "page_risk_summary.json" + } + }, + { + "category": "render_mapping_error", + "severity": "minor", + "block_ids": [ + "p1:4", + "p1:6", + "p1:7", + "p1:8", + "p1:9", + "p1:10", + "p1:11", + "p1:15", + "p1:25", + "p1:26", + "p1:27", + "p2:10", + "p4:3", + "p6:6", + "p7:3", + "p7:4", + "p9:2", + "p10:3", + "p10:5", + "p10:8" + ], + "truth": "rendered fulltext should be traceable back to source blocks", + "pipeline_behavior": "some render-default blocks are not easily mapped into the current fulltext output", + "root_cause_hypothesis": "render omission or snippet mismatch", + "evidence": { + "annotated_page": null, + "artifact": "fulltext_block_mapping_summary.json" + } + } + ] +} \ No newline at end of file diff --git a/audit/49NUE2G7/audit_report.md b/audit/49NUE2G7/audit_report.md new file mode 100644 index 00000000..e2d32985 --- /dev/null +++ b/audit/49NUE2G7/audit_report.md @@ -0,0 +1,37 @@ +# OCR Truth Audit Report - 49NUE2G7 + +- Mode: `high-risk` +- Status: `READY` +- Reviewed pages: [1, 3, 4, 5, 6, 7, 8, 10] +- Reviewed blocks: 151 + +## Findings + +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `major` `same_page_boundary_error`: page contains mixed body/reference/tail signals +- `minor` `render_mapping_error`: some render-default blocks are not easily mapped into the current fulltext output + +## Disposition Guidance + +- Use `repair` when the finding reflects a pipeline defect worth fixing now. +- Use `residual` when the finding is real but intentionally deferred. +- Do not rewrite expected truth to make current output look correct. diff --git a/audit/49NUE2G7/audit_scope.json b/audit/49NUE2G7/audit_scope.json new file mode 100644 index 00000000..d37fa9f7 --- /dev/null +++ b/audit/49NUE2G7/audit_scope.json @@ -0,0 +1,1311 @@ +{ + "mode": "high-risk", + "selected_pages": [ + 1, + 3, + 4, + 5, + 6, + 7, + 8, + 10 + ], + "required_block_ids": [ + "p1:0", + "p1:1", + "p1:2", + "p1:3", + "p1:4", + "p1:5", + "p1:6", + "p1:7", + "p1:8", + "p1:9", + "p1:10", + "p1:11", + "p1:12", + "p1:13", + "p1:14", + "p1:15", + "p1:16", + "p1:17", + "p1:18", + "p1:19", + "p1:20", + "p1:21", + "p1:22", + "p1:23", + "p1:24", + "p1:25", + "p1:26", + "p1:27", + "p3:2", + "p4:2", + "p5:2", + "p5:12", + "p6:3", + "p6:6", + "p6:11", + "p7:2", + "p7:6", + "p8:2", + "p8:4", + "p10:0", + "p10:2", + "p10:3", + "p10:4", + "p10:5", + "p10:6", + "p10:7", + "p10:8", + "p10:9", + "p10:10", + "p10:11", + "p10:12", + "p10:13", + "p10:14", + "p10:15", + "p10:16", + "p10:18", + "p10:19", + "p10:20", + "p10:21", + "p10:22", + "p10:23", + "p10:24", + "p10:25", + "p10:26", + "p10:27", + "p10:28", + "p10:29", + "p10:30", + "p10:31", + "p10:32", + "p10:33", + "p10:34", + "p10:35", + "p10:36", + "p10:37", + "p10:38", + "p10:39", + "p10:40" + ], + "required_blocks": [ + { + "block_id": "p1:0", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:1", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:2", + "page": 1, + "required_reason": [ + "frontmatter", + "needs_resolution" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:3", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:4", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:5", + "page": 1, + "required_reason": [ + "frontmatter", + "object_ownership" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:6", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:7", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:8", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:9", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:10", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:11", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:12", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:13", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:14", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:15", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:16", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:17", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:18", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:19", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:20", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:21", 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"p5:2", + "page": 5, + "required_reason": [ + "object_ownership" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p5:12", + "page": 5, + "required_reason": [ + "backmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p6:3", + "page": 6, + "required_reason": [ + "object_ownership" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p6:6", + "page": 6, + "required_reason": [ + "object_ownership" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p6:11", + "page": 6, + "required_reason": [ + "same_page_boundary" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p7:2", + "page": 7, + "required_reason": [ + "object_ownership" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p7:6", + "page": 7, + "required_reason": [ + "backmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p8:2", + "page": 8, + "required_reason": [ + "object_ownership" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p8:4", + "page": 8, + "required_reason": [ + "backmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, 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Harkey $ {}^{a} $, Anthony A. Gatti $ {}^{b} $, Mylène P. Jansen $ {}^{c} $, McKenzie S. White $ {}^{b} $, Jessica Tolzman $ {}^{a} $, Arjun Parmar $ {}^{a} $, Ian Frederick $ {}^{a}","[55.0, 378.0, 909.0, 433.0]",authors,0.8,"[""page-1 zone author_zone: Matthew S. Harkey $ {}^{a} $, Anthony A. Gatti $ {}^{b} $,""]",authors,0.8,body_zone,reference_like,citation_line,True,True +1,5,image,,"[1049.0, 334.0, 1105.0, 389.0]",media_asset,0.85,"[""media label: image""]",media_asset,0.85,frontmatter_main_zone,support_like,empty,True,True +1,6,text," $ ^{a} $ Department of Kinesiology, Michigan State University, East Lansing, MI, USA","[57.0, 441.0, 509.0, 459.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: $ ^{a} $ Department of Kinesiology, Michigan State Universit""]",affiliation,0.8,frontmatter_main_zone,support_like,affiliation_marker,True,True +1,7,text," $ ^{b} $ Department of Radiology, Stanford University, Stanford, CA, USA","[57.0, 459.0, 442.0, 476.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: $ ^{b} $ Department of Radiology, Stanford University, Stanf""]",affiliation,0.8,frontmatter_main_zone,support_like,affiliation_marker,True,True +1,8,text," $ ^{c} $ Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht, the Netherlands","[57.0, 474.0, 725.0, 492.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: $ ^{c} $ Department of Rheumatology & Clinical Immunology, U""]",affiliation,0.8,frontmatter_main_zone,support_like,affiliation_marker,True,True +1,9,text," $ ^{d} $ Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, USA","[57.0, 492.0, 637.0, 509.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: $ ^{d} $ Department of Radiology and Biomedical Imaging, Uni""]",affiliation,0.8,frontmatter_main_zone,support_like,affiliation_marker,True,True +1,10,text," $ ^{e} $ La Trobe Sport and Exercise Medicine Research Centre, La Trobe University, Melbourne, VIC, Australia","[57.0, 508.0, 652.0, 525.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: $ ^{e} $ La Trobe Sport and Exercise Medicine Research Centr""]",affiliation,0.8,frontmatter_main_zone,support_like,affiliation_marker,True,True +1,11,text,"School of Physical Therapy, Western University, London, ONT, Canada","[57.0, 527.0, 468.0, 544.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: School of Physical Therapy, Western University, London, ONT,""]",affiliation,0.8,frontmatter_main_zone,support_like,none,True,True +1,12,paragraph_title,ARTICLE INFO,"[57.0, 590.0, 255.0, 610.0]",frontmatter_noise,0.5,"[""unnumbered paragraph_title on page 1 outside title zone: ARTICLE INFO""]",section_heading,0.5,frontmatter_main_zone,support_like,short_fragment,False,False +1,13,text,"Article history: +Received 19 June 2025 +Received in revised form 10 October 2025 +Accepted 6 November 2025","[57.0, 630.0, 316.0, 700.0]",frontmatter_noise,0.8,"[""page-1 zone journal_furniture_zone: Article history:\nReceived 19 June 2025\nReceived in revised f""]",frontmatter_noise,0.8,body_zone,body_like,none,False,False +1,14,text,"Keywords: +Ultrasound +Computer Tomography +Magnetic resonance imaging +Radiography","[57.0, 721.0, 236.0, 810.0]",frontmatter_noise,0.7,"[""frontmatter noise text: Keywords:\nUltrasound\nComputer Tomography\nMagnetic resonance ""]",frontmatter_noise,0.7,body_zone,body_like,none,False,False +1,15,paragraph_title,A B S T R A C T,"[390.0, 590.0, 538.0, 610.0]",section_heading,0.5,"[""unnumbered paragraph_title on page 1 outside title zone: A B S T R A C T""]",section_heading,0.5,body_zone,body_like,short_fragment,True,True +1,16,abstract,"on how emerging methods and multi-tissue assessments are contributing to disease characterization, early detection, and intervention strategies. +Design: We conducted a comprehensive search strategy of","[388.0, 657.0, 1111.0, 818.0]",body_paragraph,0.85,"[""abstract label from Paddle OCR""]",abstract_body,0.85,body_zone,body_like,none,True,True +1,17,abstract,"Results: A total of 26 studies were included. Collectively, the studies reinforce the importance of viewing osteoarthritis as a condition involving multiple joint structures, with inflammation as a re","[389.0, 822.0, 1111.0, 955.0]",abstract_body,0.85,"[""abstract label from Paddle OCR""]",abstract_body,0.85,body_zone,body_like,none,True,True +1,18,abstract,Conclusions: Imaging research in the osteoarthritis continues to broaden in scope and application. The studies highlighted in this review illustrate how advances in methods and metrics are improving o,"[389.0, 954.0, 1109.0, 1030.0]",abstract_body,0.85,"[""abstract label from Paddle OCR""]",abstract_body,0.85,body_zone,body_like,none,True,True +1,19,text,"© 2025 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","[408.0, 1030.0, 1109.0, 1071.0]",frontmatter_noise,0.8,"[""page-1 zone journal_furniture_zone: \u00a9 2025 Osteoarthritis Research Society International. Publis""]",frontmatter_noise,0.8,body_zone,body_like,none,False,False +1,20,paragraph_title,Introduction,"[58.0, 1134.0, 163.0, 1154.0]",section_heading,0.9,"[""explicit scholarly heading: Introduction""]",section_heading,0.9,body_zone,heading_like,canonical_section_name,True,True +1,21,text,"Osteoarthritis (OA) is a heterogeneous, multi-tissue disease characterized by structural changes, inflammation, and altered joint function $ [1] $. Medical imaging plays a critical role in the assess","[56.0, 1176.0, 569.0, 1219.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,22,text,,"[595.0, 1133.0, 1111.0, 1367.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +1,23,footnote," $ ^{*} $ Correspondence to: Department of Kinesiology, Michigan State University, 308 W. Circle Drive #112, East Lansing MI, 48824.","[57.0, 1261.0, 569.0, 1298.0]",footnote,0.7,"[""footnote label: $ ^{*} $ Correspondence to: Department of Kinesiology, Michi""]",footnote,0.7,body_zone,body_like,affiliation_marker,True,True +1,24,footnote,"E-mail addresses: harkeym1@msu.edu (M. Harkey),","[72.0, 1297.0, 393.0, 1314.0]",footnote,0.7,"[""footnote label: E-mail addresses: harkeym1@msu.edu (M. Harkey),""]",footnote,0.7,body_zone,body_like,none,True,True +1,25,footnote,"aagatti@stanford.edu (A. Gatti), m.p.jansen-36@umcutrecht.nl (M. Jansen), kenziew@stanford.edu (M. White), tolzmanj@msu.edu (J. Tolzman), parmarar@msu.edu (A. Parmar), frede220@msu.edu (I. Frederick),","[57.0, 1304.0, 509.0, 1386.0]",footnote,0.7,"[""footnote label: aagatti@stanford.edu (A. Gatti), m.p.jansen-36@umcutrecht.nl""]",footnote,0.7,body_zone,body_like,none,True,True +1,26,footer,https://doi.org/10.1016/j.joca.2025.11.004,"[58.0, 1402.0, 307.0, 1419.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +1,27,footer,"1063-4584/© 2025 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","[55.0, 1417.0, 1111.0, 1455.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +2,0,header,M.S. Harkey et al. / Osteoarthritis and Cartilage 34 (2026) 28–38,"[416.0, 70.0, 797.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,frontmatter_main_zone,support_like,none,False,False +2,1,number,29,"[1112.0, 70.0, 1132.0, 86.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +2,2,text,"identify imaging features of early disease, defined as changes preceding radiographic OA (Kellgren Lawrence [KL] grade > 1), and to better characterize distinct OA subgroups [3–5].","[78.0, 107.0, 593.0, 170.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,3,text,"This narrative review aimed to identify a select number of imaging studies from the past year that highlight emerging trends, novel approaches, and clinical relevance in OA. We acknowledge that many o","[79.0, 171.0, 594.0, 424.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,4,paragraph_title,Methods,"[81.0, 443.0, 156.0, 463.0]",section_heading,0.9,"[""explicit scholarly heading: Methods""]",section_heading,0.9,body_zone,heading_like,canonical_section_name,True,True +2,5,text,"To ensure a comprehensive and unbiased selection of studies, we performed a systematic search of PubMed, Embase via EBSCO, and CINAHL via EBSCO for studies on imaging and OA with an initial search on ","[78.0, 484.0, 594.0, 1012.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,6,paragraph_title,Search results and thematic organization,"[80.0, 1032.0, 411.0, 1053.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Search results and thematic organization""]",subsection_heading,0.6,body_zone,body_like,none,True,True +2,7,text,"The initial search yielded 4842 records. After removing duplicates, we screened 3852 titles and abstracts, and 262 full-text studies met the inclusion criteria (Fig. 1). Each full-text article was ind","[78.0, 1073.0, 594.0, 1475.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,8,text,,"[618.0, 107.0, 1135.0, 256.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +2,9,paragraph_title,Major themes,"[620.0, 275.0, 738.0, 297.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Major themes""]",subsection_heading,0.6,body_zone,body_like,short_fragment,True,True +2,10,text,Theme #1: effusion-synovitis imaging,"[620.0, 317.0, 896.0, 340.0]",unknown_structural,0.8,"[""page-1 zone author_zone: Theme #1: effusion-synovitis imaging""]",authors,0.8,body_zone,body_like,none,False,True +2,11,text,Highlighted study: [11C]-PBR28 PET as a novel marker of synovial inflammation,"[618.0, 358.0, 1133.0, 401.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,12,text,Sandström et al. [6] conducted the first in vivo study using [11 C]-PBR28 PET/MRI in knee osteoarthritis (OA) to measure joint inflammation (Fig. 2). The technique targets the 18-kDa translocator prot,"[619.0, 401.0, 1135.0, 737.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,13,text,Additional Key Studies,"[644.0, 737.0, 822.0, 758.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,14,text,"• Ultrasound Effusion-Synovitis and Gait Asymmetry: Harkey et al. [7] found that 87% of individuals 1–5 years post-ACL reconstruction had ultrasound-detected effusion-synovitis, with higher effusion g","[628.0, 778.0, 1134.0, 926.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,15,text,• Early Knee OA Effusion and Symptoms: Mizuno et al. [8] used ultrasound to evaluate joint effusion and reported that even mild effusion in participants with early knee OA was associated with worse sy,"[628.0, 926.0, 1134.0, 1073.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,16,text,• Synovitis Mediates OA Progression: Deng et al. [9] used longitudinal MRI and mediation modeling to show that synovitis mediates the relationship between medial meniscus extrusion and knee OA progres,"[628.0, 1074.0, 1133.0, 1179.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,17,text,"- AI-Based Effusion Detection on Radiographs: Won et al. [10] developed an AI model to classify knee joint effusion on radiographs, using MRI-defined effusion as the reference standard. The model outp","[628.0, 1179.0, 1134.0, 1307.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,18,text,Theme summary: advancing the detection and interpretation of synovial inflammation,"[620.0, 1326.0, 1085.0, 1369.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,19,text,"The past year's work reinforces that effusion-synovitis is not merely an incidental finding but a clinically meaningful feature across the OA spectrum, from post-traumatic populations to early and est","[618.0, 1389.0, 1135.0, 1475.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,0,number,30,"[58.0, 70.0, 79.0, 86.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +3,1,header,M.S. Harkey et al. / Osteoarthritis and Cartilage 34 (2026) 28–38,"[392.0, 69.0, 774.0, 89.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,none,False,False +3,2,image,,"[141.0, 136.0, 1018.0, 1261.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +3,3,figure_title,Fig. 1,"[77.0, 1306.0, 138.0, 1330.0]",figure_caption,0.92,"[""figure_title label: Fig. 1""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +3,4,figure_title,"Flow diagram outlining the study selection process for the narrative review. A total of 4842 records were identified through database searches, with 990 duplicates removed and 262 studies assessed as ","[67.0, 1345.0, 1099.0, 1411.0]",figure_caption,0.85,"[""figure_title label: Flow diagram outlining the study selection process for the n""]",figure_caption,0.85,body_zone,legend_like,none,True,True +4,0,header,M.S. Harkey et al. / Osteoarthritis and Cartilage 34 (2026) 28–38,"[416.0, 69.0, 797.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,none,False,False +4,1,number,31,"[1111.0, 70.0, 1131.0, 87.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +4,2,image,,"[87.0, 121.0, 1120.0, 649.0]",media_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,body_like,empty,True,True +4,3,vision_footnote,"PET/MRI as a Marker of Synovial Inflammation in Knee Osteoarthritis. Representative $ [^{11}C] $-PBR28 PET/MRI images showing tracer uptake of $ [^{11}C] $-PBR28, which binds to the 18-kDa transloca","[88.0, 681.0, 1122.0, 828.0]",footnote,0.7,"[""vision_footnote label: PET/MRI as a Marker of Synovial Inflammation in Knee Osteoar""]",footnote,0.7,,unknown_like,none,True,True +4,4,text,"AI-enhanced radiography demonstrate progress in improving detection, quantification, and interpretation of synovial inflammation. Importantly, these imaging features correlate with pain and function m","[78.0, 862.0, 593.0, 1033.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,5,paragraph_title,Theme #2: infrapatellar fat pad,"[81.0, 1073.0, 313.0, 1096.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Theme #2: infrapatellar fat pad""]",subsection_heading,0.6,body_zone,body_like,none,True,True +4,6,text,Highlighted study: dynamic ultrasound evaluation of the infrapatellar fat pad,"[78.0, 1115.0, 592.0, 1158.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,7,text,Sugimoto et al. [11] advanced the field by assessing real-time morphological changes of the infrapatellar fat pad (IFP) during walking using synchronized ultrasound and 3D motion capture (Fig. 3). In ,"[77.0, 1159.0, 594.0, 1476.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,8,text,,"[619.0, 862.0, 1131.0, 906.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +4,9,text,Additional Key Studies,"[644.0, 906.0, 822.0, 927.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,10,text,• Sex- and BMI-Specific Associations Between Infrapatellar Fat Pad and Symptoms: Wagner et al. [12] found that infrapatellar fat pad abnormalities on MRI were associated with worse self-reported sympt,"[628.0, 946.0, 1133.0, 1115.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,11,text,• Infrapatellar Fat Pad Injury and Cartilage Degeneration: Harris et al. [13] showed that more severe baseline infrapatellar fat pad injury on MRI predicted greater progression of patellofemoral carti,"[627.0, 1115.0, 1134.0, 1242.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,12,text,- Radiomic Infrapatellar Fat Pad Features Predict OA and Symptoms: Khan et al. [14] used radiomics and machine learning on MRIs 10 years post-ACL reconstruction to identify infrapatellar fat pad featu,"[628.0, 1242.0, 1134.0, 1368.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,13,text,• Ultrasound Echo Intensity as a Marker of Symptom Burden: Nakayama et al. [15] reported that higher ultrasound echo intensity in the superficial medial infrapatellar fat pad was linked to knee sympto,"[628.0, 1368.0, 1134.0, 1476.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,0,number,32,"[58.0, 70.0, 79.0, 86.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +5,1,header,M.S. Harkey et al. / Osteoarthritis and Cartilage 34 (2026) 28–38,"[393.0, 69.0, 773.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,none,False,False +5,2,image,,"[255.0, 141.0, 910.0, 755.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +5,3,vision_footnote,Osteoarthritis and Cartilage,"[836.0, 791.0, 1100.0, 824.0]",footnote,0.7,"[""vision_footnote label: Osteoarthritis and Cartilage""]",footnote,0.7,body_zone,unknown_like,none,True,True +5,4,figure_title,Fig. 3,"[76.0, 798.0, 139.0, 822.0]",figure_caption,0.92,"[""figure_title label: Fig. 3""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +5,5,figure_title,Ultrasound-Based Measurement of Infrapatellar Fat Pad Morphology. Schematic representation (left) highlighting the anatomical location of the infrapatellar fat pad relative to the patellar tendon and ,"[66.0, 838.0, 1100.0, 965.0]",figure_caption,0.85,"[""figure_title label: Ultrasound-Based Measurement of Infrapatellar Fat Pad Morpho""]",figure_caption,0.85,body_zone,legend_like,none,True,True +5,6,text,"Theme summary: fat pad imaging links inflammation, mechanics, and clinical symptoms","[56.0, 989.0, 569.0, 1030.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,7,text,This year's studies highlight the multifaceted role of the infrapatellar fat pad in OA as both a biomechanical buffer and an inflammatory organ. By applying novel techniques such as dynamic ultrasound,"[55.0, 1032.0, 571.0, 1307.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,8,paragraph_title,Theme #3: muscle,"[58.0, 1327.0, 193.0, 1346.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Theme #3: muscle""]",subsection_heading,0.6,body_zone,body_like,short_fragment,True,True +5,9,text,Highlighted study: AI-based CT muscle composition and function,"[57.0, 1368.0, 526.0, 1388.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,10,text,Kono et al. [16] used an AI-based approach to analyze CT-derived muscle composition and its relationship to patient-reported outcomes in 43 patients with end-stage knee OA undergoing total knee arthro,"[56.0, 1390.0, 570.0, 1475.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,11,text,,"[595.0, 989.0, 1110.0, 1219.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +5,12,paragraph_title,Additional Key Studies,"[621.0, 1221.0, 798.0, 1241.0]",backmatter_boundary_candidate,0.5,"[""backmatter boundary candidate: Additional Key Studies""]",backmatter_boundary_candidate,0.5,body_zone,body_like,none,True,True +5,13,text,"• Intramuscular Fat and Cartilage Quality: Okada et al. [17] used two-point Dixon MRI to assess intramuscular fat infiltration in the quadriceps and found that greater fat infiltration, particularly i","[604.0, 1263.0, 1110.0, 1410.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,14,text,"• Intramuscular Fat and Muscle Weakness: Gorski et al. [18] used Dixon MRI to show that greater fat infiltration in the gluteus minimus was associated with fiber type shifts, increased collagen","[605.0, 1411.0, 1111.0, 1475.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,0,header,M.S. Harkey et al. / Osteoarthritis and Cartilage 34 (2026) 28–38,"[416.0, 69.0, 797.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,none,False,False +6,1,number,33,"[1112.0, 70.0, 1132.0, 87.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +6,2,figure_title,a,"[111.0, 139.0, 130.0, 160.0]",figure_inner_text,0.9,"[""panel label / figure inner text: a""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +6,3,image,,"[95.0, 170.0, 1113.0, 846.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,4,figure_title,b,"[650.0, 134.0, 670.0, 161.0]",figure_inner_text,0.9,"[""panel label / figure inner text: b""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +6,5,figure_title,Fig. 4,"[100.0, 883.0, 162.0, 907.0]",figure_caption,0.92,"[""figure_title label: Fig. 4""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +6,6,figure_title,"Al-Based CT Segmentation and 3D Reconstruction of Lower Limb Muscles. (A) Cross-sectional CT image at the mid-thigh level with AI-based segmentation of individual muscle groups, allowing for quantific","[90.0, 923.0, 1123.0, 1029.0]",figure_caption_candidate,0.85,"[""figure_title label: Al-Based CT Segmentation and 3D Reconstruction of Lower Limb""]",figure_caption,0.85,body_zone,legend_like,none,False,False +6,7,text,"deposition, reduced vastus lateralis activation, and lower knee extensor strength in patients with hip OA.","[101.0, 1049.0, 591.0, 1091.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,8,text,"• Normative Trends in Intramuscular Fat: Joseph et al. [19] used axial MRI data from the Osteoarthritis Initiative to establish normative intramuscular fat values using the Goutallier classification, ","[87.0, 1091.0, 593.0, 1259.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,9,text,"• Ultrasound as a Marker of Muscle Quality: Li et al. [20] showed that quadriceps ultrasound markers (e.g., echo intensity, stiffness) were elevated in knee OA-affected limbs and correlated with radio","[88.0, 1259.0, 592.0, 1367.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,10,text,Theme summary: muscle quality over size as a marker of OA risk and progression,"[80.0, 1389.0, 592.0, 1431.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,11,text,"Across modalities including CT, MRI, and ultrasound, the emerging consensus is that muscle quality, particularly intramuscular fat, is a stronger indicator of OA risk and functional decline than muscl","[79.0, 1432.0, 592.0, 1475.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,12,text,,"[618.0, 1049.0, 1134.0, 1282.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +6,13,paragraph_title,Theme #4: subchondral bone,"[621.0, 1305.0, 834.0, 1327.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Theme #4: subchondral bone""]",subsection_heading,0.6,body_zone,body_like,none,True,True +6,14,text,Highlighted study: ShapeMed-knee neural shape model benchmark,"[620.0, 1346.0, 1106.0, 1368.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,15,text,"A key advancement this year was the introduction of the ShapeMed-Knee dataset and benchmark by Gatti et al., $ [21] $ which includes over 9300 femur and cartilage meshes derived from MRI scans. This ","[618.0, 1368.0, 1133.0, 1476.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,0,number,34,"[58.0, 70.0, 79.0, 86.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +7,1,header,M.S. Harkey et al. / Osteoarthritis and Cartilage 34 (2026) 28–38,"[393.0, 69.0, 773.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,none,False,False +7,2,image,,"[70.0, 138.0, 1098.0, 435.0]",media_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,body_like,empty,True,True +7,3,vision_footnote,Overview of the ShapeMed-Knee Dataset and Neural Shape Model Benchmark Workflow. Orange Box (ShapeMed-Knee Dataset): 9376 knee MRI scans were segmented to generate bone and cartilage anatomical shapes,"[66.0, 446.0, 1098.0, 557.0]",footnote,0.7,"[""vision_footnote label: Overview of the ShapeMed-Knee Dataset and Neural Shape Model""]",footnote,0.7,body_zone,body_like,none,True,True +7,4,vision_footnote,"With permission from: Gatti et al., 2025, IEEE Transactions on Medical Imaging, ©2025 IEEE [21]. No changes were made to the original figure.","[65.0, 554.0, 1096.0, 575.0]",footnote,0.7,"[""vision_footnote label: With permission from: Gatti et al., 2025, IEEE Transactions ""]",footnote,0.7,body_zone,body_like,none,True,True +7,5,text,"reconstruction accuracy compared to traditional statistical shape models (Fig. 5). Specifically, the hybrid model reduced average surface distance errors by over 40% and showed enhanced performance in","[56.0, 611.0, 570.0, 822.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,6,paragraph_title,Additional Key Studies,"[80.0, 822.0, 258.0, 842.0]",backmatter_boundary_candidate,0.5,"[""backmatter boundary candidate: Additional Key Studies""]",backmatter_boundary_candidate,0.5,body_zone,body_like,none,True,True +7,7,text,- CT-Based Subchondral Bone Shape Modeling: Burlison et al. [22] validated the use of CT-based modeling as a reliable alternative to MRI for quantifying distal femoral bone shape. CT-derived subchondr,"[65.0, 863.0, 569.0, 989.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,8,text,- Ultrasound-Based Statistical Shape Modeling: Parmar et al. [23] developed and validated a statistical shape model using ultrasound images of the femoral trochlea to identify shape changes associated,"[64.0, 989.0, 570.0, 1180.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,9,text,• Patellofemoral Subchondral Bone Shape and Malalignment: Demirjian et al. [24] demonstrated that ACL reconstruction patients exhibit altered patellofemoral alignment and femoral trochlear shape using,"[65.0, 1179.0, 569.0, 1284.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,10,text,- Longitudinal Predictive Value of Subchondral Bone Shape: Saxer et al. [25] demonstrated that MRI-derived subchondral bone shape metrics were independently associated with the risk of knee replacemen,"[65.0, 1284.0, 570.0, 1455.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,11,text,,"[605.0, 611.0, 1110.0, 718.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +7,12,text,Theme summary: subchondral bone shape modeling across modalities and clinical contexts,"[595.0, 744.0, 1109.0, 786.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,13,text,"Across modalities including MRI, CT, and ultrasound, recent studies converge on the clinical utility of shape modeling to quantify subchondral bone morphology, track disease progression, and stratify ","[595.0, 787.0, 1111.0, 1061.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,14,paragraph_title,Theme #5: subcutaneous fat,"[597.0, 1094.0, 805.0, 1115.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Theme #5: subcutaneous fat""]",subsection_heading,0.6,body_zone,body_like,none,True,True +7,15,text,Highlighted study: knee-adjacent subcutaneous fat and structural decline,"[596.0, 1137.0, 1109.0, 1178.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,16,text,"Joseph et al., [27] conducted a large-scale cross-sectional analysis using the full Osteoarthritis Initiative baseline MRI dataset (n = 4796) to evaluate whether local subcutaneous fat—defined as adip","[595.0, 1180.0, 1110.0, 1455.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +8,0,header,M.S. Harkey et al. / Osteoarthritis and Cartilage 34 (2026) 28–38,"[416.0, 69.0, 797.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,none,False,False +8,1,number,35,"[1112.0, 70.0, 1132.0, 87.0]",noise,0.9,"[""page number label""]",noise,0.9,,unknown_like,short_fragment,False,False +8,2,image,,"[249.0, 139.0, 965.0, 556.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,,unknown_like,empty,True,True +8,3,figure_title,"MRI-Based Measurement of Knee Subcutaneous Fat Thickness. A coronal reformation of the DESS sequence showing subcutaneous fat thickness measurements at the medial femur, medial tibia, lateral femur, a","[91.0, 635.0, 1122.0, 742.0]",figure_caption,0.85,"[""figure_title label: MRI-Based Measurement of Knee Subcutaneous Fat Thickness. A ""]",figure_caption,0.85,,legend_like,none,True,True +8,4,paragraph_title,Additional Key Studies,"[104.0, 779.0, 280.0, 801.0]",backmatter_boundary_candidate,0.5,"[""backmatter boundary candidate: Additional Key Studies""]",backmatter_boundary_candidate,0.5,,unknown_like,none,True,True +8,5,text,• Subcutaneous Fat and Cartilage Lesions: Hart et al. [28] found that greater subcutaneous fat thickness on knee MRI at one-year post-ACL reconstruction predicted worsening tibiofemoral and patellofem,"[89.0, 820.0, 593.0, 946.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +8,6,text,"• Subcutaneous Fat and Long-Term Symptoms: Michaud et al. [29] found that subcutaneous knee fat thickness decreased on average from one to five years post-ACL reconstruction, while BMI and waist circu","[88.0, 947.0, 593.0, 1094.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +8,7,text,• Subcutaneous Fat Changes Linked to Radiographic Progression: Lee et al. [30] conducted a case-control study of individuals with baseline KL grades 0–3 and found greater two-year increases in thigh s,"[89.0, 1095.0, 592.0, 1242.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +8,8,text,"• Ultrasound Estimation of Body Fat: Tolzman et al. [31] validated a method for estimating body fat using ultrasound-measured thigh fat thickness, accurately predicting DXA-derived body fat in collegi","[87.0, 1242.0, 593.0, 1349.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +8,9,text,Theme summary: local subcutaneous fat as a distinct and actionable imaging marker,"[80.0, 1368.0, 591.0, 1409.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +8,10,text,"Emerging evidence consistently supports that regional subcutaneous fat surrounding the knee, rather than BMI alone, relates to early OA risk, cartilage deterioration, and potentially functional declin","[79.0, 1411.0, 594.0, 1475.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +8,11,text,,"[618.0, 778.0, 1134.0, 970.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,,unknown_like,empty,True,True +8,12,paragraph_title,Cross-cutting themes in Oa imaging,"[620.0, 990.0, 910.0, 1011.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Cross-cutting themes in Oa imaging""]",subsection_heading,0.6,body_zone,unknown_like,none,True,True +8,13,text,Recent research in OA imaging has underscored that disease processes extend across multiple joint structures and can be understood through several recurring themes. Building on the studies highlighted,"[618.0, 1031.0, 1134.0, 1287.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +8,14,text,"1. OA affects multiple joint structures. The past year's work reinforces that OA is a condition involving the whole joint, with meaningful imaging findings reported across subchondral bone, effusion-s","[623.0, 1304.0, 1134.0, 1476.0]",body_paragraph,0.6,"[""reference-like pattern: 1. OA affects multiple joint structures. The past year's wor""]",reference_item,0.6,,reference_like,reference_numeric_dot,True,True +9,0,number,36,"[59.0, 71.0, 79.0, 86.0]",noise,0.9,"[""page number label""]",noise,0.9,,unknown_like,short_fragment,False,False +9,1,header,M.S. Harkey et al. / Osteoarthritis and Cartilage 34 (2026) 28–38,"[393.0, 70.0, 773.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,none,False,False +9,2,text,"was linked to symptom burden and radiographic progression $ [6,8,9] $, fat pad changes to altered mechanics and inflammation $ [11–13] $, and muscle quality and local adiposity to structural alterat","[79.0, 107.0, 569.0, 254.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +9,3,text,"2. Inflammation is a unifying OA feature. Inflammatory processes were consistently observed across diverse joint structures using modalities such as PET, ultrasound, and radiography. Over the past yea","[59.0, 254.0, 570.0, 485.0]",body_paragraph,0.6,"[""reference-like pattern: 2. Inflammation is a unifying OA feature. Inflammatory proce""]",reference_item,0.6,,reference_like,reference_numeric_dot,True,True +9,4,text,"3. Accessible tools broaden OA imaging. The use of ultrasound and automated, AI-based image analysis highlights how OA imaging is becoming more scalable and clinically applicable. Quantitative ultraso","[60.0, 485.0, 570.0, 715.0]",body_paragraph,0.6,"[""reference-like pattern: 3. Accessible tools broaden OA imaging. The use of ultrasoun""]",reference_item,0.6,,unknown_like,heading_numbered,True,True +9,5,text,4. Structure and biomechanics are becoming more integrated. A growing number of studies are pairing imaging biomarkers with biomechanical data to examine how tissue-level pathology affects movement an,"[59.0, 716.0, 570.0, 950.0]",body_paragraph,0.6,"[""reference-like pattern: 4. Structure and biomechanics are becoming more integrated. ""]",reference_item,0.6,,reference_like,reference_numeric_dot,True,True +9,6,paragraph_title,Future directions in Oa imaging research,"[57.0, 968.0, 386.0, 990.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Future directions in Oa imaging research""]",subsection_heading,0.6,body_zone,unknown_like,none,True,True +9,7,text,"Building on the insights from recent studies, future directions in OA imaging are focused on translating research advancements into more scalable, predictive, and patient-centered applications. Across","[54.0, 1010.0, 570.0, 1243.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +9,8,text,"1. Clinical integration of AI-driven imaging biomarkers. AI has opened new frontiers in OA imaging by enabling large-scale, automated quantification of structural and compositional features across div","[60.0, 1262.0, 570.0, 1475.0]",body_paragraph,0.6,"[""reference-like pattern: 1. Clinical integration of AI-driven imaging biomarkers. AI ""]",reference_item,0.6,,reference_like,reference_numeric_dot,True,True +9,9,text,,"[618.0, 107.0, 1110.0, 274.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,,unknown_like,empty,True,True +9,10,text,"2. Track biomechanical drivers of imaging changes. As structural imaging becomes more sensitive and quantitative, there is increasing recognition that biomechanics must be more fully integrated with i","[596.0, 276.0, 1111.0, 632.0]",body_paragraph,0.6,"[""reference-like pattern: 2. Track biomechanical drivers of imaging changes. As struct""]",reference_item,0.6,,reference_like,reference_numeric_dot,True,True +9,11,text,"3. Standardize imaging protocols across modalities. The field of OA imaging is rapidly diversifying, but methodological inconsistency remains a major barrier to synthesis and scalability. For ultrasou","[596.0, 632.0, 1111.0, 1011.0]",body_paragraph,0.6,"[""reference-like pattern: 3. Standardize imaging protocols across modalities. The fiel""]",reference_item,0.6,,reference_like,reference_numeric_dot,True,True +9,12,text,"4. Post-injury imaging to guide precision prevention. Post-traumatic OA remains a major research priority [47], yet a persistent challenge is the heterogeneity in how individuals respond to joint inju","[596.0, 1010.0, 1111.0, 1370.0]",body_paragraph,0.6,"[""reference-like pattern: 4. Post-injury imaging to guide precision prevention. Post-t""]",reference_item,0.6,,reference_like,reference_numeric_dot,True,True +9,13,paragraph_title,Conclusion,"[597.0, 1389.0, 691.0, 1410.0]",section_heading,0.9,"[""explicit scholarly heading: Conclusion""]",section_heading,0.9,body_zone,heading_like,canonical_section_name,True,True +9,14,text,"Imaging in the OA field has long recognized OA as a condition involving the whole joint, but recent work highlights rapid advances","[595.0, 1431.0, 1110.0, 1475.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,unknown_like,none,True,True +10,0,header,M.S. Harkey et al. / Osteoarthritis and Cartilage 34 (2026) 28–38,"[416.0, 70.0, 796.0, 88.0]",reference_item,0.9,"[""header label""]",noise,0.9,reference_zone,unknown_like,none,True,True +10,1,number,37,"[1112.0, 71.0, 1132.0, 87.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +10,2,text,"in imaging across multiple tissues, underscoring a more comprehensive, systems-level approach to joint assessment. This review highlights recent advances across subchondral bone, muscle, fat pads, syn","[79.0, 107.0, 594.0, 424.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,body_like,none,True,True +10,3,paragraph_title,Author contribution,"[80.0, 444.0, 246.0, 465.0]",unknown_structural,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Author contribution""]",subsection_heading,0.6,tail_nonref_hold_zone,unknown_like,short_fragment,False,True +10,4,text,All authors meet the four ICMJE authorship criteria. Each has made substantial contributions to the manuscript and accepts accountability for the accuracy and integrity of the work.,"[80.0, 487.0, 592.0, 551.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,True,True +10,5,table,"
ContributionAuthors (initials)
Conception & design of the reviewMH, AG, MJ, MW, HH, JT, AP, IF, TL
Abstract & title screening","[91.0, 572.0, 581.0, 796.0]",media_asset,0.85,"[""media label: table""]",media_asset,0.85,,reference_like,none,True,True +10,6,text,Osteoarthritis and Cartilage,"[320.0, 827.0, 584.0, 853.0]",structured_insert_candidate,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,False,False +10,7,text,Guarantors of the work:,"[106.0, 925.0, 291.0, 946.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,True,True +10,8,paragraph_title,"• Matthew S. Harkey, PhD, ATC (harkeym1@msu.edu)","[89.0, 967.0, 497.0, 989.0]",unknown_structural,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: \u2022 Matthew S. Harkey, PhD, ATC (harkeym1@msu.edu)""]",subsection_heading,0.6,tail_nonref_hold_zone,heading_like,none,False,True +10,9,paragraph_title,Appendix A. Supporting information,"[620.0, 107.0, 916.0, 129.0]",reference_item,0.5,"[""backmatter boundary candidate: Appendix A. Supporting information""]",backmatter_boundary_candidate,0.5,reference_zone,reference_like,citation_line,True,True +10,10,text,"Dr. Harkey takes overall responsibility for the integrity of the work, from inception to published article, and will address any questions regarding its accuracy or integrity.","[80.0, 1009.0, 592.0, 1074.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,True,True +10,11,paragraph_title,Declaration of Generative AI and AI-assisted technologies in the writing process,"[80.0, 1093.0, 587.0, 1136.0]",backmatter_boundary_candidate,0.5,"[""backmatter boundary candidate: Declaration of Generative AI and AI-assisted technologies in""]",backmatter_boundary_candidate,0.5,,unknown_like,none,True,True +10,12,text,"During the preparation of this work the author used ChatGPT (OpenAI) to assist with editing and improving the clarity of the manuscript text. After using this tool, the author reviewed and edited the ","[79.0, 1155.0, 593.0, 1263.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,body_like,none,True,True +10,13,paragraph_title,Disclosures,"[81.0, 1283.0, 177.0, 1304.0]",sub_subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level sub_subsection_heading: Disclosures""]",sub_subsection_heading,0.6,tail_nonref_hold_zone,unknown_like,short_fragment,True,True +10,14,text,"MSH was supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (grant number: K01 AR081389). AAG is a shareholder of NeuralSeg, GeminiOV, and NodeAI.","[79.0, 1325.0, 591.0, 1390.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,True,True +10,15,paragraph_title,Acknowledgements,"[81.0, 1411.0, 240.0, 1431.0]",sub_subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level sub_subsection_heading: Acknowledgements""]",sub_subsection_heading,0.6,tail_nonref_hold_zone,unknown_like,short_fragment,True,True +10,16,text,None.,"[105.0, 1453.0, 155.0, 1473.0]",unknown_structural,0.3,"[""short text, uncertain role""]",unknown_structural,0.3,,unknown_like,short_fragment,False,True +10,17,text,Supplementary data associated with this article can be found in the online version at doi:10.1016/j.joca.2025.11.004.,"[619.0, 149.0, 1132.0, 192.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,18,paragraph_title,References,"[622.0, 212.0, 713.0, 233.0]",reference_heading,0.9,"[""references heading: References""]",reference_heading,0.9,reference_zone,unknown_like,short_fragment,True,True +10,19,reference_content,"[1] Sa Tang, C. 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"block_id": "p11:31", + "page": 11, + "role": "reference_item", + "zone": "reference_zone", + "reason": "logical_order_between_reference_members" + }, + { + "block_id": "p11:32", + "page": 11, + "role": "reference_item", + "zone": "reference_zone", + "reason": "logical_order_between_reference_members" + } + ] + } +} \ No newline at end of file diff --git a/audit/53B47JM8/audit_report.json b/audit/53B47JM8/audit_report.json new file mode 100644 index 00000000..0dd19021 --- /dev/null +++ b/audit/53B47JM8/audit_report.json @@ -0,0 +1,547 @@ +{ + "paper_key": "53B47JM8", + "mode": "high-risk", + "status": "READY", + "focus": [], + "artifact_fingerprint": { + "result_json_hash": "sha256:e3cd579efe8f824b301ce710c7f68b4154466fb44f9aff6d31b52c2fad1ebd23", + "meta_json_hash": "sha256:47b1734a69dd63a6b6ac7160f7684dbecdd6760e8714a257fd20a51eb4f8a92d", + "blocks_raw_hash": "sha256:1cc675d44ba10794c73a11176e43c625771bb2d60e1a2cf3d82519cd13dc0b8e", + "structured_blocks_hash": 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"p6:0", + "p6:1", + "p6:2", + "p6:3", + "p6:4", + "p6:5", + "p6:6", + "p6:7", + "p6:8", + "p6:9", + "p6:10", + "p6:11", + "p6:12", + "p6:13", + "p6:14", + "p6:15", + "p6:16", + "p6:17", + "p6:18", + "p7:0", + "p7:1", + "p7:2", + "p7:3", + "p7:4", + "p7:5", + "p7:6", + "p7:7", + "p7:8", + "p7:9", + "p8:0", + "p8:1", + "p8:2", + "p8:3", + "p8:4", + "p8:5", + "p8:6", + "p8:7", + "p8:8", + "p8:9", + "p8:10", + "p8:11", + "p8:12", + "p8:13", + "p8:14", + "p8:15", + "p9:0", + "p9:1", + "p9:2", + "p9:3", + "p9:4", + "p9:5", + "p9:6", + "p9:7", + "p9:8", + "p9:9", + "p9:10", + "p9:11", + "p9:12", + "p9:13", + "p9:14", + "p9:15", + "p9:16", + "p9:17", + "p9:18", + "p9:19", + "p9:20", + "p9:21", + "p9:22", + "p9:23", + "p9:24", + "p9:25", + "p9:26", + "p9:27", + "p9:28", + "p9:29", + "p9:30", + "p9:31", + "p9:32", + "p9:33", + "p9:34", + "p9:35", + "p9:36", + "p9:37", + "p9:38", + "p11:0", + "p11:1", + "p11:2", + "p11:3", + "p11:4", + "p11:5", + "p11:6", + "p11:7", + "p11:8", + "p11:9", + "p11:10", + "p11:11", + "p11:12", + "p11:13", + "p11:14", + "p11:15", + "p11:16", + "p11:17", + "p11:18", + "p11:19", + "p11:20", + "p11:21", + "p11:22" + ], + "findings": [ + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:15" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:16" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:17" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:18" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:19" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:20" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:21" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:22" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:23" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:24" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:25" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:26" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:27" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:28" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:29" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:30" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:31" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:32" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:33" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p9:34" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "same_page_boundary_error", + "severity": "major", + "block_ids": [], + "truth": "body/reference/backmatter boundaries should be explainable at block level", + "pipeline_behavior": "page contains mixed body/reference/tail signals", + "root_cause_hypothesis": "same-page boundary ambiguity", + "evidence": { + "annotated_page": "annotated_pages/page_009.png", + "artifact": "page_risk_summary.json" + } + }, + { + "category": "render_mapping_error", + "severity": "minor", + "block_ids": [ + "p1:1", + "p1:2", + "p1:3", + "p1:5", + "p1:9", + "p1:10", + "p1:11", + "p1:12", + "p1:13", + "p1:14", + "p1:15", + "p1:16", + "p1:17", + "p1:20", + "p1:26", + "p1:27", + "p1:28", + "p1:30", + "p2:0", + "p2:1" + ], + "truth": "rendered fulltext should be traceable back to source blocks", + "pipeline_behavior": "some render-default blocks are not easily mapped into the current fulltext output", + "root_cause_hypothesis": "render omission or snippet mismatch", + "evidence": { + "annotated_page": null, + "artifact": "fulltext_block_mapping_summary.json" + } + } + ] +} \ No newline at end of file diff --git a/audit/53B47JM8/audit_report.md b/audit/53B47JM8/audit_report.md new file mode 100644 index 00000000..29750b08 --- /dev/null +++ b/audit/53B47JM8/audit_report.md @@ -0,0 +1,37 @@ +# OCR Truth Audit Report - 53B47JM8 + +- Mode: `high-risk` +- Status: `READY` +- Reviewed pages: [1, 2, 6, 7, 8, 9, 11] +- Reviewed blocks: 154 + +## Findings + +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `major` `same_page_boundary_error`: page contains mixed body/reference/tail signals +- `minor` `render_mapping_error`: some render-default blocks are not easily mapped into the current fulltext output + +## Disposition Guidance + +- Use `repair` when the finding reflects a pipeline defect worth fixing now. +- Use `residual` when the finding is real but intentionally deferred. +- Do not rewrite expected truth to make current output look correct. diff --git a/audit/53B47JM8/audit_scope.json b/audit/53B47JM8/audit_scope.json new file mode 100644 index 00000000..91a0c94b --- /dev/null +++ b/audit/53B47JM8/audit_scope.json @@ -0,0 +1,1590 @@ +{ + "mode": "high-risk", + "selected_pages": [ + 1, + 2, + 6, + 7, + 8, + 9, + 11 + ], + "required_block_ids": [ + "p1:0", + "p1:1", + "p1:2", + "p1:3", + "p1:4", + "p1:5", + "p1:6", + "p1:7", + "p1:8", + "p1:9", + "p1:10", + "p1:11", + "p1:12", + "p1:13", + "p1:14", + "p1:15", + "p1:16", + "p1:17", + "p1:18", + "p1:19", + "p1:20", + "p1:21", + "p1:22", + "p1:23", + "p1:24", + "p1:25", + "p1:26", + "p1:27", + "p1:28", + "p1:29", + "p1:30", + "p2:13", + "p6:2", + "p6:3", + "p6:4", + "p6:5", + "p6:10", + "p6:13", + "p6:14", + "p6:15", + "p6:16", + "p7:5", + "p7:6", + "p7:7", + "p8:6", + "p8:7", + 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By combining this treatment with tissue-engineering approaches (which rely on biomaterial scaffolds to construct art,"[397.0, 733.0, 1120.0, 966.0]",body_paragraph,0.85,"[""abstract label from Paddle OCR""]",abstract_body,0.85,body_zone,body_like,none,True,True +1,22,paragraph_title,1. Introduction,"[72.0, 1023.0, 198.0, 1043.0]",section_heading,0.85,"[""paragraph_title label with numbering: 1. Introduction""]",section_heading,0.85,body_zone,body_like,heading_numbered,True,True +1,23,text,"Reconstruction of large/major bone defects remains a significant challenge in modern medicine $ [1,2] $. Until now, the gold standard has been to use auto- or allo-grafts, which suffer from problems ","[69.0, 1065.0, 581.0, 1232.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,24,text,"Several biomaterials including hydrogels, naturally-derived biomaterials, synthetic polymers (e.g. poly(lactic-co-glycolic acid), poly(lactic acid), polycaprolactone, etc.) [7–9] in combination with c","[70.0, 1233.0, 581.0, 1276.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,25,text,,"[605.0, 1022.0, 1120.0, 1276.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +1,26,footnote,"* Corresponding author. Department of Mechanical Engineering, University of Connecticut, Storrs, CT, 06269, USA.","[80.0, 1322.0, 835.0, 1345.0]",footnote,0.7,"[""footnote label: * Corresponding author. Department of Mechanical Engineering""]",footnote,0.7,body_zone,body_like,none,True,True +1,27,footnote,E-mail address: nguyentd@uconn.edu (T.D. Nguyen).,"[81.0, 1342.0, 442.0, 1363.0]",footnote,0.7,"[""footnote label: E-mail address: nguyentd@uconn.edu (T.D. Nguyen).""]",footnote,0.7,body_zone,body_like,none,True,True +1,28,footnote, $ ^{1} $ Denotes equally contributed Authors.,"[81.0, 1361.0, 344.0, 1380.0]",footnote,0.7,"[""footnote label: $ ^{1} $ Denotes equally contributed Authors.""]",footnote,0.7,body_zone,body_like,affiliation_marker,True,True +1,29,footnote,https://doi.org/10.1016/j.nanoen.2020.105028,"[71.0, 1394.0, 384.0, 1413.0]",frontmatter_noise,0.8,"[""page-1 zone journal_furniture_zone: https://doi.org/10.1016/j.nanoen.2020.105028""]",frontmatter_noise,0.8,body_zone,body_like,none,False,False +1,30,footer,"Received 26 March 2020; Received in revised form 6 May 2020; Accepted 27 May 2020 +Available online 27 June 2020 +2211-2855/© 2020 Elsevier Ltd. All rights reserved.","[70.0, 1405.0, 648.0, 1469.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +2,0,header,R. Das et al.,"[71.0, 70.0, 146.0, 87.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +2,1,header,Nano Energy 76 (2020) 105028,"[937.0, 70.0, 1120.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +2,2,text,render ES limited in clinical applications and combination with tissue engineering approaches.,"[70.0, 107.0, 581.0, 148.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,3,text,"Piezoelectric materials, a group of “smart” materials which produce electricity under applied force, can be used as a self-powered scaffold that can utilize body movements or external mechanical vibra","[68.0, 151.0, 582.0, 609.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,4,text,"Consequently, the development of biodegradable piezoelectric materials becomes important to offer novel biomaterials that can generate electrical charges to promote bone regeneration and safely degrad","[68.0, 610.0, 582.0, 944.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,5,text,"The nanofibers not only offer an extracellular matrix (ECM)-like environment [35–37] but are also biodegradable to avoid the need for any removal procedures and facilitate tissue in-growth, an advance","[68.0, 944.0, 582.0, 1155.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,6,text,,"[606.0, 107.0, 1120.0, 190.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +2,7,paragraph_title,2. Experimental section,"[607.0, 211.0, 802.0, 232.0]",section_heading,0.85,"[""paragraph_title label with numbering: 2. Experimental section""]",section_heading,0.85,body_zone,reference_like,reference_numeric_dot,True,True +2,8,paragraph_title,2.1. Preparation of PLLA nanofiber mat,"[608.0, 253.0, 893.0, 274.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.1. Preparation of PLLA nanofiber mat""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +2,9,text,"The poly(L-lactic acid) (PLLA) nanofiber mat was fabricated by electrospinning as described in our previous work [32]. PLLA (PUR-ASORB PL38) was purchased from Corbion Purac (Amsterdam, Netherlands). ","[606.0, 295.0, 1120.0, 819.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,10,paragraph_title,2.2. Characterization of PLLA film,"[609.0, 840.0, 857.0, 861.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.2. Characterization of PLLA film""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +2,11,text,SEM: Scanning Electron Microscopy (SEM) was performed on mats prepared to observe the orientation of the PLLA fibers and the microstructure of the mats. Square shaped PLLA films with a dimension of 7m,"[606.0, 882.0, 1120.0, 1111.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,12,text,Measurement of the piezoelectric property and ultrasound receiving capability of the PLLA films: A force sensor was fabricated to test the,"[606.0, 1113.0, 1121.0, 1155.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,13,image,,"[74.0, 1184.0, 815.0, 1463.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +2,14,figure_title,"Fig. 1. The use of biodegradable piezoelectric PLLA nanofibers in combination with non-invasive ultrasound (US) to produce well-controlled, on-demand and stable surface charge (i.e. electrical stimula","[826.0, 1179.0, 1119.0, 1466.0]",figure_caption,0.92,"[""figure_title label: Fig. 1. The use of biodegradable piezoelectric PLLA nanofibe""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +2,15,number,2,"[589.0, 1513.0, 603.0, 1528.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +3,0,header,R. Das et al.,"[71.0, 70.0, 145.0, 87.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +3,1,header,Nano Energy 76 (2020) 105028,"[938.0, 70.0, 1120.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +3,2,text,"piezoelectric property of the PLLA film. The treated PLLA films were cut at a 45° angle with the fiber direction films with a dimension of 1.27 cm long, 1.27 cm wide to maximize the shear force under ","[69.0, 108.0, 582.0, 441.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,3,text,Film degradation study: This study was designed to determine the functional lifetime of the piezoelectric PLLA nanofiber mat. The objective of this experiment is to determine how long the PLLA mat ret,"[69.0, 444.0, 582.0, 1028.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,4,paragraph_title,2.2.1. Preparation of PLLA scaffolds for ADSC culture,"[71.0, 1050.0, 453.0, 1068.0]",sub_subsection_heading,0.85,"[""paragraph_title label with numbering: 2.2.1. Preparation of PLLA scaffolds for ADSC culture""]",sub_subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +3,5,text,The scaffolds were prepared by electrospinning as previously described. The scaffolds used as the experimental group were spun at 3000-rpm and 1000-rpm (i.e. piezoelectric samples and less-piezoelectr,"[69.0, 1070.0, 581.0, 1237.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,6,paragraph_title,2.3. Sterilization of the PLLA scaffolds and preparation of the cell culture plates to seed ADSCs,"[69.0, 1259.0, 569.0, 1300.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.3. Sterilization of the PLLA scaffolds and preparation of ""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +3,7,text,"The scaffolds prepared were sterilized using ethanol and UV treatment. The entire process was carried out under a laminar flow cell culture hood. First, the scaffolds were soaked in 70% ethanol for 30","[68.0, 1322.0, 581.0, 1466.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,8,text,"Once the whole process of sterilization was completed, the scaffolds are fixed onto 6-well culture plates (purchased from Thermo Scientific) using biocompatible silicone glue (KWIK-SIL produced by Wor","[92.0, 1468.0, 581.0, 1488.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,9,text,,"[607.0, 107.0, 1120.0, 338.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +3,10,paragraph_title,2.4. ADSC culture,"[609.0, 359.0, 745.0, 379.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.4. ADSC culture""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +3,11,text,Cells were seeded onto the PLLA scaffolds after they were sterilized and glued to the well plates. The cells used for this purpose were adipose derived stem cells (ADSCs) that were purchased from iXCe,"[607.0, 399.0, 1119.0, 926.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,12,paragraph_title,2.5. Ultrasonic (US) treatment on the ADSCs,"[608.0, 945.0, 927.0, 965.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.5. Ultrasonic (US) treatment on the ADSCs""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +3,13,text,The US treatment on the cells was started a day after the cells were put in osteogenic media. The treatment was performed using a sonication cleaning bath (Branson 2800 CPX series). The ultrasound pro,"[606.0, 988.0, 1120.0, 1195.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,14,text,"First, we taped the lid onto 4 sides of the plate using labelling tape. Then we removed the plate from the cell hood and encapsulated it in two layers of plastic wrap (Kirkland Signature Stretch-Tite ","[606.0, 1197.0, 1120.0, 1489.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,15,number,3,"[589.0, 1514.0, 603.0, 1528.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +4,0,header,R. Das et al.,"[72.0, 70.0, 145.0, 87.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +4,1,header,Nano Energy 76 (2020) 105028,"[938.0, 70.0, 1120.0, 87.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +4,2,text,"laboratory clamp, stand apparatus and an alligator clip. The plate was suspended so that it was submerged halfway into the water and horizontally level. The plate was sonicated for 20 min. When the 20","[70.0, 107.0, 581.0, 295.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,3,text,"After 10 days of treatment, the cultures were terminated and analyzed for osteogenic differentiation activity. The assays performed are Alkaline phosphatase (ALP) enzyme quantification, polymerase cha","[69.0, 358.0, 582.0, 527.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,4,paragraph_title,2.6. Bone regeneration assays,"[71.0, 317.0, 284.0, 337.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.6. Bone regeneration assays""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +4,5,paragraph_title,2.7. BCA assay,"[71.0, 547.0, 188.0, 567.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.7. BCA assay""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +4,6,text,BCA assay was used to quantify the total protein content of the cultures and this quantity was used to normalize the results of ALP and Alizarin red quantification. Protein was extracted from the cult,"[69.0, 589.0, 582.0, 757.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,7,paragraph_title,2.8. ALP quantification assay,"[71.0, 777.0, 283.0, 798.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.8. ALP quantification assay""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +4,8,text,The Alkaline phosphatase quantification was carried out using a kit purchased from Biorad (cat no-172-1063). The kit has a p-Nitrophenyl Phosphate (pNPP) based quantification technique. The protein so,"[69.0, 819.0, 582.0, 1051.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,9,paragraph_title,2.9. Alizarin red assay,"[71.0, 1071.0, 237.0, 1091.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.9. Alizarin red assay""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +4,10,text,"For the Alizarin red assay, the cultures (after removing the media) were fixed in 70% ethanol at 4 °C for 1 h. Following this, the ethanol was removed, the wells were rinsed and the Alizarin red dye (","[69.0, 1112.0, 581.0, 1343.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,11,paragraph_title,2.10. PCR quantification,"[70.0, 1364.0, 251.0, 1385.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.10. PCR quantification""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +4,12,text,PCR (polymerase chain reaction) quantification was performed using the universal sybr green master mix manufactured by Bio-rad. The primers used were osterix (forward sequence of 5'-GGA AAG GAG GCA CA,"[68.0, 1406.0, 581.0, 1488.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,13,text,,"[607.0, 108.0, 1120.0, 419.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +4,14,paragraph_title,2.11. BMSC reporter cell usage,"[609.0, 442.0, 832.0, 463.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.11. BMSC reporter cell usage""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +4,15,text,"Apart from our ADSC cultures, we also used a fluorescent reporter cell system to confirm the osteogenic properties of our materials which allowed us to monitor the proliferation and differentiation of","[606.0, 484.0, 1120.0, 736.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,16,paragraph_title,2.12. Preparation of PLLA scaffolds for BMSCs,"[609.0, 756.0, 942.0, 777.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.12. Preparation of PLLA scaffolds for BMSCs""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +4,17,text,The groups used were the same as those for the ADSC cultures. The scaffolds were prepared by electrospinning as previously described. The scaffolds used as the experimental group were spun at 3000-rpm,"[607.0, 798.0, 1120.0, 925.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,18,paragraph_title,2.13. Sterilization of the PLLA scaffolds and preparation of the cell culture plates to seed BMSCs,"[608.0, 945.0, 1075.0, 987.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.13. Sterilization of the PLLA scaffolds and preparation of""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +4,19,text,The scaffolds prepared were sterilized using 70% ethanol and UV and attached to 6 well plates using biocompatible silicone glue in the same way as described previously for the ADSC cultures and in viv,"[607.0, 1007.0, 1119.0, 1092.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,20,paragraph_title,2.14. BMSC culture,"[609.0, 1113.0, 756.0, 1133.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.14. BMSC culture""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +4,21,text,Primary BMSCs were harvested from the bone marrow of 3-4-week-old dual transgenic mice containing BSP-GFP-topaz and DMP1-RFP-mCherry fluorescent reporter genes. The hind legs of the mice were harveste,"[607.0, 1154.0, 1120.0, 1490.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,22,number,4,"[590.0, 1514.0, 602.0, 1528.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +5,0,header,R. Das et al.,"[71.0, 70.0, 145.0, 87.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +5,1,header,Nano Energy 76 (2020) 105028,"[937.0, 70.0, 1120.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +5,2,text,"cells were allowed to attach for one day under proliferation media. After that, the proliferation medium was replaced with osteogenic differentiation medium that was prepared by adding 50 $ \mu $g/ml","[70.0, 106.0, 581.0, 233.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,3,paragraph_title,2.15. Ultrasonic (US) treatment on the BMSCs,"[70.0, 253.0, 400.0, 273.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.15. Ultrasonic (US) treatment on the BMSCs""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +5,4,text,The US treatment was done on the reporter cell seeded scaffolds in the same manner as the ADSC seeded scaffolds. The culture plate was sealed using plastic wrap and duct tape and half suspended into t,"[69.0, 295.0, 582.0, 422.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,5,paragraph_title,2.16. Fluorescence microscopy and image processing,"[70.0, 442.0, 436.0, 463.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.16. Fluorescence microscopy and image processing""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +5,6,text,"At days 0 (pre-seeding), 1, 2 and 3 of US treatment, reporter cell fluorescence (N = 3) was captured using the Zeiss Axio Observer Z.1 inverted fluorescence microscope. The fluorescence of the cells w","[69.0, 483.0, 582.0, 736.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,7,paragraph_title,2.17. Preparation of PLLA scaffolds for the in vivo experiment on mice,"[71.0, 757.0, 562.0, 777.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.17. Preparation of PLLA scaffolds for the in vivo experime""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +5,8,text,"The scaffolds used were prepared by electrospinning and then cutting out squares from the electro spun films at the dimensions of $ 4 \, mm \times 4 \, mm $. The scaffolds that were used as the exper","[68.0, 798.0, 581.0, 946.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,9,paragraph_title,2.18. Sterilization of the PLLA scaffolds for the implantation,"[71.0, 966.0, 492.0, 987.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.18. Sterilization of the PLLA scaffolds for the implantati""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +5,10,text,"The scaffolds prepared were cut into $ 4 \, mm \times 4 \, mm $ pieces and sterilized using 70% ethanol and UV in the same way as described previously for the ADSC cultures.","[69.0, 1008.0, 581.0, 1072.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,11,paragraph_title,2.19. Implantation surgery to demonstrate the osteoinductive property of the PLLA nanofiber film,"[70.0, 1092.0, 571.0, 1133.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.19. Implantation surgery to demonstrate the osteoinductive""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +5,12,text,The surgical procedure has been approved by the institutional Animal Use Committee (Protocol # 101815-0421). Six transgenic NSG mice containing Collagen 3.6 -GFP-topaz fluorescent genes (Charlse River,"[68.0, 1154.0, 583.0, 1490.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,13,text,,"[607.0, 108.0, 1120.0, 275.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +5,14,paragraph_title,2.20. US treatment on the animals,"[609.0, 295.0, 855.0, 315.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.20. US treatment on the animals""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +5,15,text,"The US treatment was received by the animals for 30 min a day, 5 days a week, 4 weeks in total. The US transducer used for this experiment was a bolt clamped langevin transducer that operated at 40 kH","[607.0, 337.0, 1120.0, 694.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,16,paragraph_title,2.21. Sample collection,"[609.0, 714.0, 779.0, 734.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.21. Sample collection""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +5,17,text,"Two weeks after the termination of the US treatment, the animals were euthanized and their calvarial bone (Fig. S2) was harvested to look for evidence of bone regeneration inside the defect.","[607.0, 756.0, 1119.0, 819.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,18,paragraph_title,2.22. Histology,"[609.0, 840.0, 725.0, 861.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.22. Histology""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +5,19,text,"The harvested calvaria bone was fixed in 10% neutral neutral-buffered formalin (Sigma) at 4 °C overnight, rinsed with PBS (1X) three times, and then soaked in 30% sucrose (Sigma) in deionized water at","[606.0, 882.0, 1120.0, 1238.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,20,paragraph_title,3. Results and discussions,"[609.0, 1259.0, 822.0, 1279.0]",section_heading,0.85,"[""paragraph_title label with numbering: 3. Results and discussions""]",section_heading,0.85,body_zone,body_like,heading_numbered,True,True +5,21,text,"We used electrospinning to create the piezoelectric PLLA nanofiber mats and post-process the films by annealing and cutting at $ 45^{\circ} $ to achieve piezoelectric PLLA nanofibers, following our p","[606.0, 1301.0, 1120.0, 1490.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,22,number,5,"[589.0, 1515.0, 602.0, 1528.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +6,0,header,R. Das et al.,"[71.0, 70.0, 145.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +6,1,header,Nano Energy 76 (2020) 105028,"[937.0, 70.0, 1120.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +6,2,image,,"[155.0, 109.0, 487.0, 439.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,3,chart,,"[158.0, 442.0, 490.0, 578.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,4,chart,,"[157.0, 580.0, 498.0, 818.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,5,chart,,"[157.0, 819.0, 491.0, 1068.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,6,figure_title,Fig. 2. Characterization of the microstructure and piezoelectric performance of the PLLA nanofiber mats under applied ultrasound (US). a. Schematic of the electrospinning setup used to fabricate the P,"[69.0, 1083.0, 582.0, 1315.0]",figure_caption,0.92,"[""figure_title label: Fig. 2. Characterization of the microstructure and piezoelec""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +6,7,text,"significantly higher output voltage than the ones produced at 1000 rpm while the signal is smallest for the samples made at 300 rpm under the same applied US (see Fig. 2b and c, and S1). Therefore, we","[69.0, 1337.0, 583.0, 1486.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,8,text,,"[607.0, 107.0, 1120.0, 462.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +6,9,text,"Importantly, we carried out in vitro experiments to study osteogenesis of stem cells grown on the scaffolds. Fig. 3a and Fig. S3 describes our in vitro experiment in which we apply US (40 KHz, 20 min/","[607.0, 463.0, 1120.0, 632.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,10,chart,,"[617.0, 658.0, 1100.0, 835.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,11,figure_title,b,"[618.0, 834.0, 634.0, 856.0]",figure_inner_text,0.9,"[""panel label / figure inner text: b""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +6,12,figure_title,C,"[858.0, 840.0, 874.0, 858.0]",figure_inner_text,0.9,"[""panel label / figure inner text: C""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +6,13,chart,,"[619.0, 844.0, 856.0, 1039.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,14,chart,,"[860.0, 856.0, 1112.0, 1036.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,15,chart,,"[619.0, 1041.0, 858.0, 1221.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,16,chart,,"[860.0, 1043.0, 1113.0, 1221.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,17,figure_title,"Fig. 3. Osteogenic differentiation of stem cells, grown on the piezoelectric PLLA nanofiber scaffold under applied US in vitro. a. A simple schematic demonstrates our setup for seeding adipose stem ce","[606.0, 1241.0, 1120.0, 1488.0]",figure_caption,0.92,"[""figure_title label: Fig. 3. Osteogenic differentiation of stem cells, grown on t""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +6,18,number,6,"[589.0, 1515.0, 602.0, 1529.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +7,0,header,R. Das et al.,"[71.0, 70.0, 145.0, 87.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +7,1,header,Nano Energy 76 (2020) 105028,"[937.0, 70.0, 1120.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +7,2,text,"of stem cells for combination with our PLLA nanofibers (if needed in the future) to construct a tissue scaffold. We used three nanofiber films of 3000-rpm (piezo. sample), 1000-rpm (less-piezo. sample","[68.0, 106.0, 583.0, 652.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,3,text,,"[606.0, 107.0, 1121.0, 482.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +7,4,text,"In addition to ADSCs, we also confirmed the ability of our piezoelectric nanofiber scaffold under applied US to induce osteogenesis from bone marrow stem cells (BMSCs) with reporter genes in vitro, as","[606.0, 483.0, 1120.0, 653.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,5,image,,"[75.0, 679.0, 783.0, 1468.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +7,6,chart,,"[80.0, 1143.0, 409.0, 1464.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +7,7,chart,,"[425.0, 1133.0, 784.0, 1466.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +7,8,figure_title,Fig. 4. Osteogenic activity of reporter bone marrow stem cells (BMSCs) when grown on the electrospun PLLA scaffolds with US treatment. a. Schematic to demonstrate the progressive expression from BSP t,"[799.0, 678.0, 1119.0, 1025.0]",figure_caption,0.92,"[""figure_title label: Fig. 4. Osteogenic activity of reporter bone marrow stem cel""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +7,9,number,7,"[589.0, 1514.0, 602.0, 1528.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +8,0,header,R. Das et al.,"[71.0, 70.0, 146.0, 87.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,short_fragment,False,False +8,1,header,Nano Energy 76 (2020) 105028,"[937.0, 70.0, 1120.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,none,False,False +8,2,text,electrospun scaffolds (same groups as for the ADSC cultures). Fig. 4a demonstrates schematically the progressive expression from BSP to DMP for the BMSCs that undergo osteogenic differentiation and ch,"[68.0, 106.0, 583.0, 610.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +8,3,text,"To further demonstrate the osteo-inductive property of the surface charge produced by our biodegradable piezoelectric nanofibers, we performed an in vivo proof of concept experiment, as seen in Fig. 5","[68.0, 609.0, 582.0, 758.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +8,4,text,,"[606.0, 105.0, 1121.0, 759.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,,unknown_like,empty,True,True +8,5,figure_title,a,"[123.0, 791.0, 148.0, 818.0]",figure_inner_text,0.9,"[""panel label / figure inner text: a""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +8,6,image,,"[127.0, 781.0, 362.0, 947.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,,unknown_like,empty,True,True +8,7,image,,"[364.0, 789.0, 585.0, 951.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,,unknown_like,empty,True,True +8,8,image,,"[618.0, 791.0, 811.0, 951.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,,unknown_like,empty,True,True +8,9,image,,"[834.0, 791.0, 1063.0, 950.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,,unknown_like,empty,True,True +8,10,image,,"[125.0, 993.0, 357.0, 1297.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,,unknown_like,empty,True,True +8,11,image,,"[359.0, 993.0, 594.0, 1299.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,,unknown_like,empty,True,True +8,12,image,,"[595.0, 983.0, 827.0, 1298.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,,unknown_like,empty,True,True +8,13,image,,"[831.0, 980.0, 1066.0, 1299.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,,unknown_like,empty,True,True +8,14,figure_title,Fig. 5. Representative histology sections of the mouse calvarial bone showing details of bone formation and cell migration into the defects for the groups of piezo-scaffold (3000 rpm) and non-piezo. s,"[69.0, 1317.0, 1121.0, 1490.0]",figure_caption,0.92,"[""figure_title label: Fig. 5. Representative histology sections of the mouse calva""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +8,15,number,8,"[589.0, 1514.0, 603.0, 1528.0]",noise,0.9,"[""page number label""]",noise,0.9,,unknown_like,short_fragment,False,False +9,0,header,R. Das et al.,"[71.0, 70.0, 145.0, 87.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +9,1,header,Nano Energy 76 (2020) 105028,"[937.0, 70.0, 1120.0, 88.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +9,2,text,"osteoblast activity in a region [63,64]. Therefore, the green Collagen 3.6 fluorescent signals allow us to visualize the number of osteoblast-like cells at the defect site. Fig. 5c (iii) clearly shows","[69.0, 107.0, 582.0, 420.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,3,text,"In brief, the in vivo results clearly illustrate that the group 1 with the piezoelectric scaffold and ultrasound (US) strongly induce mineral/bone formation, ALP release and osteoblast migration. Thes","[69.0, 421.0, 581.0, 547.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,4,paragraph_title,4. Conclusions,"[71.0, 567.0, 195.0, 587.0]",section_heading,0.85,"[""paragraph_title label with numbering: 4. Conclusions""]",section_heading,0.85,body_zone,body_like,heading_numbered,True,True +9,5,text,"We have presented a novel tissue electrical-stimulation approach, using the biodegradable piezoelectric PLLA nanofiber scaffold with non-invasive US to generate controllable surface charges, consequen","[68.0, 608.0, 583.0, 985.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,body_like,none,True,True +9,6,text,"Despite such a significant advantage, further studies and optimizations of the presented tissue-stimulation approach are still required. First, an optimal amount of piezoelectric charge for osteogenes","[68.0, 986.0, 583.0, 1447.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,body_like,none,True,True +9,7,paragraph_title,Data statement,"[609.0, 108.0, 733.0, 127.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Data statement""]",subsection_heading,0.6,body_zone,body_like,short_fragment,True,True +9,8,text,"The experimental data, presented herein, are available for sharing upon a reasonable request.","[607.0, 149.0, 1118.0, 191.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,9,paragraph_title,Declaration of competing interest,"[608.0, 211.0, 875.0, 232.0]",backmatter_boundary_candidate,0.5,"[""backmatter boundary candidate: Declaration of competing interest""]",backmatter_boundary_candidate,0.5,body_zone,body_like,none,True,True +9,10,text,Authors declare no competing interests.,"[632.0, 253.0, 921.0, 273.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,11,paragraph_title,CRediT authorship contribution statement,"[608.0, 294.0, 942.0, 315.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: CRediT authorship contribution statement""]",subsection_heading,0.6,body_zone,body_like,none,True,True +9,12,text,"Ritopa Das: Conceptualization, Methodology, Data curation, Formal analysis, Writing - original draft, Writing - review & editing. Eli J. Curry: Data curation, Formal analysis, Writing - review & editi","[606.0, 337.0, 1120.0, 632.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,13,paragraph_title,Acknowledgements,"[609.0, 651.0, 765.0, 672.0]",sub_subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level sub_subsection_heading: Acknowledgements""]",sub_subsection_heading,0.6,body_zone,body_like,short_fragment,True,True +9,14,text,The work is supported by the NIH (Grant # 1R21AR075196 and # 1R21AR075133). Guleid Awale is supported by NIH (supplementary grant #R21EB024787-02S1). The authors thank Allison Taylor and Jessica Horny,"[607.0, 692.0, 1120.0, 799.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,15,paragraph_title,Appendix A. Supplementary data,"[608.0, 818.0, 875.0, 839.0]",reference_item,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Appendix A. Supplementary data""]",subsection_heading,0.6,reference_zone,reference_like,citation_line,True,True +9,16,text,Supplementary data to this article can be found online at https://doi.org/10.1016/j.nanoen.2020.105028.,"[607.0, 860.0, 1116.0, 902.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,17,paragraph_title,References,"[610.0, 923.0, 700.0, 943.0]",reference_heading,0.9,"[""references heading: References""]",reference_heading,0.9,reference_zone,unknown_like,short_fragment,True,True +9,18,reference_content,"[1] A.R. Amini, C.T. Laurencin, S.P. Nukavarapu, Crit. Rev. Biomed. Eng. 40 (2012) 363–408.","[617.0, 962.0, 1106.0, 993.0]",reference_item,0.85,"[""reference content label: [1] A.R. Amini, C.T. Laurencin, S.P. Nukavarapu, Crit. Rev. ""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +9,19,reference_content,"[2] T.W. Bauer, G.F. Muschler, Clin. Orthop. Relat. Res. 371 (2000) 10–27.","[617.0, 996.0, 1059.0, 1013.0]",reference_item,0.85,"[""reference content label: [2] T.W. Bauer, G.F. Muschler, Clin. Orthop. Relat. Res. 371""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +9,20,reference_content,"[3] C. Laurencin, Y. Khan, S.F. El-Amin, Expet Rev. Med. Dev. 3 (2006) 49–57.","[618.0, 1013.0, 1082.0, 1027.0]",reference_item,0.85,"[""reference content label: [3] C. Laurencin, Y. Khan, S.F. El-Amin, Expet Rev. Med. Dev""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +9,21,reference_content,"[4] C.T. Laurencin, A. Ambrosio, M. Borden, J. Cooper Jr., Annu. Rev. Biomed. Eng. 1 (1999) 19–46.","[618.0, 1027.0, 1113.0, 1057.0]",reference_item,0.85,"[""reference content label: [4] C.T. Laurencin, A. Ambrosio, M. Borden, J. Cooper Jr., A""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +9,22,reference_content,"[5] C.T. Laurencin, Y. Khan, Regenerative Engineering, American Association for the Advancement of Science, 2012.","[619.0, 1058.0, 1111.0, 1089.0]",reference_item,0.85,"[""reference content label: [5] C.T. Laurencin, Y. Khan, Regenerative Engineering, Ameri""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +9,23,reference_content,"[6] G. Narayanan, V.N. Vernekar, E.L. Kuyinu, C.T. Laurencin, Adv. Drug Deliv. Rev. 107 (2016) 247–276.","[618.0, 1090.0, 1111.0, 1121.0]",reference_item,0.85,"[""reference content label: [6] G. Narayanan, V.N. Vernekar, E.L. Kuyinu, C.T. Laurencin""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +9,24,reference_content,"[7] N.M. Martinelli, M.J.G. Ribeiro, R. Ricci, M.A. Marques, A.O. Lobo, F.R. 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Introduction", + "found_in_fulltext": true, + "fulltext_offset": 1744 + }, + { + "block_id": "p1:23", + "page": 1, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Reconstruction of large/major bone defects remains a significant challenge in mo", + "found_in_fulltext": true, + "fulltext_offset": 1760 + }, + { + "block_id": "p1:24", + "page": 1, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Several biomaterials including hydrogels, naturally-derived biomaterials, synthe", + "found_in_fulltext": true, + "fulltext_offset": 2277 + }, + { + "block_id": "p1:26", + "page": 1, + "role": "footnote", + "zone": "body_zone", + "render_default": true, + "snippet": "* Corresponding author. Department of Mechanical Engineering, University of Conn", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p1:27", + "page": 1, + "role": "footnote", + "zone": "body_zone", + "render_default": true, + "snippet": "E-mail address: nguyentd@uconn.edu (T.D. Nguyen).", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p1:28", + "page": 1, + "role": "footnote", + "zone": "body_zone", + "render_default": true, + "snippet": "$ ^{1} $ Denotes equally contributed Authors.", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p1:30", + "page": 1, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "Received 26 March 2020; Received in revised form 6 May 2020; Accepted 27 May 202", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p2:0", + "page": 2, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "R. Das et al.", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p2:1", + "page": 2, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "Nano Energy 76 (2020) 105028", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p2:2", + "page": 2, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "render ES limited in clinical applications and combination with tissue engineeri", + "found_in_fulltext": true, + "fulltext_offset": 3264 + }, + { + "block_id": "p2:3", + "page": 2, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Piezoelectric materials, a group of “smart” materials which produce electricity ", + "found_in_fulltext": true, + "fulltext_offset": 3359 + }, + { + "block_id": "p2:4", + "page": 2, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Consequently, the development of biodegradable piezoelectric materials becomes i", + "found_in_fulltext": true, + "fulltext_offset": 4869 + }, + { + "block_id": "p2:5", + "page": 2, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The nanofibers not only offer an extracellular matrix (ECM)-like environment [35", + "found_in_fulltext": true, + "fulltext_offset": 5953 + }, + { + "block_id": "p2:7", + "page": 2, + "role": "section_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2. Experimental section", + "found_in_fulltext": true, + "fulltext_offset": 6865 + }, + { + "block_id": "p2:8", + "page": 2, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.1. Preparation of PLLA nanofiber mat", + "found_in_fulltext": true, + "fulltext_offset": 6893 + }, + { + "block_id": "p2:9", + "page": 2, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The poly(L-lactic acid) (PLLA) nanofiber mat was fabricated by electrospinning a", + "found_in_fulltext": true, + "fulltext_offset": 6932 + }, + { + "block_id": "p2:10", + "page": 2, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.2. Characterization of PLLA film", + "found_in_fulltext": true, + "fulltext_offset": 8615 + }, + { + "block_id": "p2:11", + "page": 2, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "SEM: Scanning Electron Microscopy (SEM) was performed on mats prepared to observ", + "found_in_fulltext": true, + "fulltext_offset": 8650 + }, + { + "block_id": "p2:12", + "page": 2, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Measurement of the piezoelectric property and ultrasound receiving capability of", + "found_in_fulltext": true, + "fulltext_offset": 9338 + }, + { + "block_id": "p2:15", + "page": 2, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "2", + "found_in_fulltext": true, + "fulltext_offset": 387 + }, + { + "block_id": "p3:0", + "page": 3, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "R. Das et al.", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p3:1", + "page": 3, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "Nano Energy 76 (2020) 105028", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p3:2", + "page": 3, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "piezoelectric property of the PLLA film. The treated PLLA films were cut at a 45", + "found_in_fulltext": true, + "fulltext_offset": 9527 + }, + { + "block_id": "p3:3", + "page": 3, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Film degradation study: This study was designed to determine the functional life", + "found_in_fulltext": true, + "fulltext_offset": 10610 + }, + { + "block_id": "p3:4", + "page": 3, + "role": "sub_subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.2.1. Preparation of PLLA scaffolds for ADSC culture", + "found_in_fulltext": true, + "fulltext_offset": 12476 + }, + { + "block_id": "p3:5", + "page": 3, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The scaffolds were prepared by electrospinning as previously described. The scaf", + "found_in_fulltext": true, + "fulltext_offset": 12530 + }, + { + "block_id": "p3:6", + "page": 3, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.3. Sterilization of the PLLA scaffolds and preparation of the cell culture pla", + "found_in_fulltext": true, + "fulltext_offset": 13018 + }, + { + "block_id": "p3:7", + "page": 3, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The scaffolds prepared were sterilized using ethanol and UV treatment. The entir", + "found_in_fulltext": true, + "fulltext_offset": 13116 + }, + { + "block_id": "p3:8", + "page": 3, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Once the whole process of sterilization was completed, the scaffolds are fixed o", + "found_in_fulltext": true, + "fulltext_offset": 13567 + }, + { + "block_id": "p3:10", + "page": 3, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.4. ADSC culture", + "found_in_fulltext": true, + "fulltext_offset": 14425 + }, + { + "block_id": "p3:11", + "page": 3, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Cells were seeded onto the PLLA scaffolds after they were sterilized and glued t", + "found_in_fulltext": true, + "fulltext_offset": 14443 + }, + { + "block_id": "p3:12", + "page": 3, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.5. Ultrasonic (US) treatment on the ADSCs", + "found_in_fulltext": true, + "fulltext_offset": 16175 + }, + { + "block_id": "p3:13", + "page": 3, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The US treatment on the cells was started a day after the cells were put in oste", + "found_in_fulltext": true, + "fulltext_offset": 16219 + }, + { + "block_id": "p3:14", + "page": 3, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "First, we taped the lid onto 4 sides of the plate using labelling tape. Then we ", + "found_in_fulltext": true, + "fulltext_offset": 16862 + }, + { + "block_id": "p3:15", + "page": 3, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "3", + "found_in_fulltext": true, + "fulltext_offset": 2041 + }, + { + "block_id": "p4:0", + "page": 4, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "R. Das et al.", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p4:1", + "page": 4, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "Nano Energy 76 (2020) 105028", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p4:2", + "page": 4, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "laboratory clamp, stand apparatus and an alligator clip. The plate was suspended", + "found_in_fulltext": true, + "fulltext_offset": 17884 + }, + { + "block_id": "p4:3", + "page": 4, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "After 10 days of treatment, the cultures were terminated and analyzed for osteog", + "found_in_fulltext": true, + "fulltext_offset": 18500 + }, + { + "block_id": "p4:4", + "page": 4, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.6. Bone regeneration assays", + "found_in_fulltext": true, + "fulltext_offset": 19019 + }, + { + "block_id": "p4:5", + "page": 4, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.7. BCA assay", + "found_in_fulltext": true, + "fulltext_offset": 19053 + }, + { + "block_id": "p4:6", + "page": 4, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "BCA assay was used to quantify the total protein content of the cultures and thi", + "found_in_fulltext": true, + "fulltext_offset": 19068 + }, + { + "block_id": "p4:7", + "page": 4, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.8. ALP quantification assay", + "found_in_fulltext": true, + "fulltext_offset": 19625 + }, + { + "block_id": "p4:8", + "page": 4, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The Alkaline phosphatase quantification was carried out using a kit purchased fr", + "found_in_fulltext": true, + "fulltext_offset": 19655 + }, + { + "block_id": "p4:9", + "page": 4, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.9. Alizarin red assay", + "found_in_fulltext": true, + "fulltext_offset": 20421 + }, + { + "block_id": "p4:10", + "page": 4, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "For the Alizarin red assay, the cultures (after removing the media) were fixed i", + "found_in_fulltext": true, + "fulltext_offset": 20445 + }, + { + "block_id": "p4:11", + "page": 4, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.10. PCR quantification", + "found_in_fulltext": true, + "fulltext_offset": 21157 + }, + { + "block_id": "p4:12", + "page": 4, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "PCR (polymerase chain reaction) quantification was performed using the universal", + "found_in_fulltext": true, + "fulltext_offset": 21182 + }, + { + "block_id": "p4:14", + "page": 4, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.11. BMSC reporter cell usage", + "found_in_fulltext": true, + "fulltext_offset": 22442 + }, + { + "block_id": "p4:15", + "page": 4, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Apart from our ADSC cultures, we also used a fluorescent reporter cell system to", + "found_in_fulltext": true, + "fulltext_offset": 22473 + }, + { + "block_id": "p4:16", + "page": 4, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.12. Preparation of PLLA scaffolds for BMSCs", + "found_in_fulltext": true, + "fulltext_offset": 23278 + }, + { + "block_id": "p4:17", + "page": 4, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The groups used were the same as those for the ADSC cultures. The scaffolds were", + "found_in_fulltext": true, + "fulltext_offset": 23324 + }, + { + "block_id": "p4:18", + "page": 4, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.13. Sterilization of the PLLA scaffolds and preparation of the cell culture pl", + "found_in_fulltext": true, + "fulltext_offset": 23732 + }, + { + "block_id": "p4:19", + "page": 4, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The scaffolds prepared were sterilized using 70% ethanol and UV and attached to ", + "found_in_fulltext": true, + "fulltext_offset": 23831 + }, + { + "block_id": "p4:20", + "page": 4, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.14. BMSC culture", + "found_in_fulltext": true, + "fulltext_offset": 24050 + }, + { + "block_id": "p4:21", + "page": 4, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Primary BMSCs were harvested from the bone marrow of 3-4-week-old dual transgeni", + "found_in_fulltext": true, + "fulltext_offset": 24069 + }, + { + "block_id": "p4:22", + "page": 4, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "4", + "found_in_fulltext": true, + "fulltext_offset": 2043 + }, + { + "block_id": "p5:0", + "page": 5, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "R. Das et al.", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p5:1", + "page": 5, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "Nano Energy 76 (2020) 105028", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p5:2", + "page": 5, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "cells were allowed to attach for one day under proliferation media. After that, ", + "found_in_fulltext": true, + "fulltext_offset": 15721 + }, + { + "block_id": "p5:3", + "page": 5, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.15. Ultrasonic (US) treatment on the BMSCs", + "found_in_fulltext": true, + "fulltext_offset": 25625 + }, + { + "block_id": "p5:4", + "page": 5, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The US treatment was done on the reporter cell seeded scaffolds in the same mann", + "found_in_fulltext": true, + "fulltext_offset": 25670 + }, + { + "block_id": "p5:5", + "page": 5, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.16. Fluorescence microscopy and image processing", + "found_in_fulltext": true, + "fulltext_offset": 26062 + }, + { + "block_id": "p5:6", + "page": 5, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "At days 0 (pre-seeding), 1, 2 and 3 of US treatment, reporter cell fluorescence ", + "found_in_fulltext": true, + "fulltext_offset": 26113 + }, + { + "block_id": "p5:7", + "page": 5, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.17. Preparation of PLLA scaffolds for the in vivo experiment on mice", + "found_in_fulltext": true, + "fulltext_offset": 26908 + }, + { + "block_id": "p5:8", + "page": 5, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The scaffolds used were prepared by electrospinning and then cutting out squares", + "found_in_fulltext": true, + "fulltext_offset": 26979 + }, + { + "block_id": "p5:9", + "page": 5, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.18. Sterilization of the PLLA scaffolds for the implantation", + "found_in_fulltext": true, + "fulltext_offset": 27481 + }, + { + "block_id": "p5:10", + "page": 5, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The scaffolds prepared were cut into $ 4 \\, mm \\times 4 \\, mm $ pieces and steri", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p5:11", + "page": 5, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.19. Implantation surgery to demonstrate the osteoinductive property of the PLL", + "found_in_fulltext": true, + "fulltext_offset": 27720 + }, + { + "block_id": "p5:12", + "page": 5, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The surgical procedure has been approved by the institutional Animal Use Committ", + "found_in_fulltext": true, + "fulltext_offset": 27817 + }, + { + "block_id": "p5:14", + "page": 5, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.20. US treatment on the animals", + "found_in_fulltext": true, + "fulltext_offset": 29470 + }, + { + "block_id": "p5:15", + "page": 5, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The US treatment was received by the animals for 30 min a day, 5 days a week, 4 ", + "found_in_fulltext": true, + "fulltext_offset": 29504 + }, + { + "block_id": "p5:16", + "page": 5, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.21. Sample collection", + "found_in_fulltext": true, + "fulltext_offset": 30645 + }, + { + "block_id": "p5:17", + "page": 5, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Two weeks after the termination of the US treatment, the animals were euthanized", + "found_in_fulltext": true, + "fulltext_offset": 30669 + }, + { + "block_id": "p5:18", + "page": 5, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "2.22. Histology", + "found_in_fulltext": true, + "fulltext_offset": 30864 + }, + { + "block_id": "p5:19", + "page": 5, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The harvested calvaria bone was fixed in 10% neutral neutral-buffered formalin (", + "found_in_fulltext": true, + "fulltext_offset": 30880 + }, + { + "block_id": "p5:20", + "page": 5, + "role": "section_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "3. Results and discussions", + "found_in_fulltext": true, + "fulltext_offset": 32046 + }, + { + "block_id": "p5:21", + "page": 5, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "We used electrospinning to create the piezoelectric PLLA nanofiber mats and post", + "found_in_fulltext": true, + "fulltext_offset": 32073 + }, + { + "block_id": "p5:22", + "page": 5, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "5", + "found_in_fulltext": true, + "fulltext_offset": 427 + }, + { + "block_id": "p6:0", + "page": 6, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "R. Das et al.", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p6:1", + "page": 6, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "Nano Energy 76 (2020) 105028", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p6:7", + "page": 6, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "significantly higher output voltage than the ones produced at 1000 rpm while the", + "found_in_fulltext": true, + "fulltext_offset": 32708 + }, + { + "block_id": "p6:9", + "page": 6, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Importantly, we carried out in vitro experiments to study osteogenesis of stem c", + "found_in_fulltext": true, + "fulltext_offset": 34362 + }, + { + "block_id": "p6:18", + "page": 6, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "6", + "found_in_fulltext": true, + "fulltext_offset": 409 + }, + { + "block_id": "p7:0", + "page": 7, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "R. 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Fig. 4a demonstrat", + "found_in_fulltext": true, + "fulltext_offset": 38695 + }, + { + "block_id": "p8:3", + "page": 8, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "To further demonstrate the osteo-inductive property of the surface charge produc", + "found_in_fulltext": true, + "fulltext_offset": 40376 + }, + { + "block_id": "p8:15", + "page": 8, + "role": "noise", + "zone": "", + "render_default": false, + "snippet": "8", + "found_in_fulltext": true, + "fulltext_offset": 430 + }, + { + "block_id": "p9:0", + "page": 9, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "R. 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Conclusions", + "found_in_fulltext": true, + "fulltext_offset": 44507 + }, + { + "block_id": "p9:5", + "page": 9, + "role": "body_paragraph", + "zone": "tail_nonref_hold_zone", + "render_default": true, + "snippet": "We have presented a novel tissue electrical-stimulation approach, using the biod", + "found_in_fulltext": true, + "fulltext_offset": 44522 + }, + { + "block_id": "p9:6", + "page": 9, + "role": "body_paragraph", + "zone": "tail_nonref_hold_zone", + "render_default": true, + "snippet": "Despite such a significant advantage, further studies and optimizations of the p", + "found_in_fulltext": true, + "fulltext_offset": 45728 + }, + { + "block_id": "p9:7", + "page": 9, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "Data statement", + "found_in_fulltext": true, + "fulltext_offset": 47236 + }, + { + "block_id": "p9:8", + "page": 9, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The experimental data, presented herein, are available for sharing upon a reason", + "found_in_fulltext": true, + "fulltext_offset": 47251 + }, + { + "block_id": "p9:9", + "page": 9, + "role": "backmatter_boundary_candidate", + "zone": "body_zone", + "render_default": true, + "snippet": "Declaration of competing interest", + "found_in_fulltext": true, + "fulltext_offset": 47345 + }, + { + "block_id": "p9:10", + "page": 9, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Authors declare no competing interests.", + "found_in_fulltext": true, + "fulltext_offset": 47379 + }, + { + "block_id": "p9:11", + "page": 9, + "role": "subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "CRediT authorship contribution statement", + "found_in_fulltext": true, + "fulltext_offset": 47422 + }, + { + "block_id": "p9:12", + "page": 9, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Ritopa Das: Conceptualization, Methodology, Data curation, Formal analysis, Writ", + "found_in_fulltext": true, + "fulltext_offset": 47463 + }, + { + "block_id": "p9:13", + "page": 9, + "role": "sub_subsection_heading", + "zone": "body_zone", + "render_default": true, + "snippet": "Acknowledgements", + "found_in_fulltext": true, + "fulltext_offset": 48407 + }, + { + "block_id": "p9:14", + "page": 9, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "The work is supported by the NIH (Grant # 1R21AR075196 and # 1R21AR075133). 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"block_ids": [ + "p13:2" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:3" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:4" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:5" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:6" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:7" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:8" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:9" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:10" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:11" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:12" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:13" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:14" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:15" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:16" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:17" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:18" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:19" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p13:20" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "render_mapping_error", + "severity": "minor", + "block_ids": [ + "p1:4", + "p1:5", + "p1:6", + "p1:11", + "p1:19", + "p1:20", + "p2:0", + "p2:1", + "p3:0", + "p4:0", + "p4:4", + "p5:0", + "p5:2", + "p6:0", + "p7:0", + "p7:5", + "p8:0", + "p8:5", + "p9:0", + "p9:1" + ], + "truth": "rendered fulltext should be traceable back to source blocks", + "pipeline_behavior": "some render-default blocks are not easily mapped into the current fulltext output", + "root_cause_hypothesis": "render omission or snippet mismatch", + "evidence": { + "annotated_page": null, + "artifact": "fulltext_block_mapping_summary.json" + } + } + ] +} \ No newline at end of file diff --git a/audit/62LTMCI8/audit_report.md b/audit/62LTMCI8/audit_report.md new file mode 100644 index 00000000..eb7d080b --- /dev/null +++ b/audit/62LTMCI8/audit_report.md @@ -0,0 +1,36 @@ +# OCR Truth Audit Report - 62LTMCI8 + +- Mode: `high-risk` +- Status: `READY` +- Reviewed pages: [1, 4, 5, 6, 7, 8, 9, 11, 13] +- Reviewed blocks: 105 + +## Findings + +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `minor` `render_mapping_error`: some render-default blocks are not easily mapped into the current fulltext output + +## Disposition Guidance + +- Use `repair` when the finding reflects a pipeline defect worth fixing now. +- Use `residual` when the finding is real but intentionally deferred. +- Do not rewrite expected truth to make current output look correct. diff --git 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+1,0,header_image,,"[70.0, 98.0, 237.0, 168.0]",non_body_insert,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,frontmatter_main_zone,support_like,empty,False,False +1,1,header_image,,"[1030.0, 109.0, 1120.0, 169.0]",non_body_insert,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,frontmatter_main_zone,support_like,empty,False,False +1,2,text,Review,"[67.0, 207.0, 134.0, 231.0]",non_body_insert,0.3,"[""short text, uncertain role""]",unknown_structural,0.3,frontmatter_main_zone,support_like,short_fragment,False,False +1,3,doc_title,Electrically Conductive Hydrogels for Articular Cartilage Tissue Engineering,"[66.0, 232.0, 1007.0, 313.0]",paper_title,0.8,"[""page-1 zone title_zone: Electrically Conductive Hydrogels for Articular Cartilage Ti""]",paper_title,0.8,frontmatter_main_zone,support_like,none,True,True +1,4,text,"Filipe Miguel $ ^{1,2} $, Frederico Barbosa $ ^{1,2} $, Frederico Castelo Ferreira $ ^{1,2,*} $ and João Carlos Silva $ ^{1,2,*} $","[66.0, 334.0, 969.0, 362.0]",authors,0.8,"[""page-1 zone author_zone: Filipe Miguel $ ^{1,2} $, Frederico Barbosa $ ^{1,2} $, Fr""]",authors,0.8,frontmatter_main_zone,support_like,none,True,True +1,5,text,"iBB—Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa,","[326.0, 402.0, 977.0, 446.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: iBB\u2014Institute for Bioengineering and Biosciences and Departm""]",affiliation,0.8,frontmatter_main_zone,support_like,none,True,True +1,6,text,"2 Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico,","[327.0, 448.0, 1026.0, 476.0]",affiliation,0.8,"[""page-1 zone affiliation_zone: 2 Associate Laboratory i4HB\u2014Institute for Health and Bioecon""]",affiliation,0.8,body_zone,reference_like,reference_numeric_dot,True,True +1,7,text,"check for updates +* Correspondence: frederico.ferreira@tecnico.ulisboa.pt (F.C.F.); joao.f.da.silva@tecnico.ulisboa.pt (J.C.S.)","[70.0, 853.0, 179.0, 889.0]",frontmatter_noise,0.8,"[""page-1 zone journal_furniture_zone: check for updates\n* Correspondence: frederico.ferreira@tecni""]",frontmatter_noise,0.8,frontmatter_main_zone,support_like,none,False,False +1,8,text,,"[327.0, 491.0, 1087.0, 514.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,frontmatter_main_zone,support_like,empty,True,True +1,9,text,"Citation: Miguel, F.; Barbosa, F.; Ferreira, F.C.; Silva, J.C. Electrically Conductive Hydrogels for Articular Cartilage Tissue Engineering. Gels 2022, 8, 710. https://doi.org/10.3390/gels8110710","[66.0, 897.0, 296.0, 1039.0]",frontmatter_noise,0.8,"[""page-1 zone journal_furniture_zone: Citation: Miguel, F.; Barbosa, F.; Ferreira, F.C.; Silva, J.""]",frontmatter_noise,0.8,frontmatter_main_zone,support_like,none,False,False +1,10,text,"Received: 4 October 2022 +Accepted: 1 November 2022 +Published: 3 November 2022","[67.0, 1114.0, 252.0, 1183.0]",frontmatter_noise,0.8,"[""page-1 zone journal_furniture_zone: Received: 4 October 2022\nAccepted: 1 November 2022\nPublished""]",frontmatter_noise,0.8,body_zone,body_like,none,False,False +1,11,text,Academic Editors: Junfeng Shi and Fei Xu,"[67.0, 1052.0, 291.0, 1097.0]",frontmatter_support,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,12,text,Publisher's Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.,"[66.0, 1197.0, 307.0, 1289.0]",frontmatter_noise,0.88,"[""default body_paragraph for text label"", ""late role resolution: editorial phrase cross-validates non-body classification"", ""zone=body_zone"", ""style_family=support_like""]",body_paragraph,0.6,body_zone,support_like,none,False,False +1,13,image,,"[69.0, 1313.0, 185.0, 1354.0]",media_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +1,14,abstract,"Abstract: Articular cartilage is a highly specialized tissue found in diarthrodial joints, which is crucial for healthy articular motion. Despite its importance, articular cartilage has limited regene","[327.0, 540.0, 1124.0, 878.0]",abstract_body,0.85,"[""abstract label from Paddle OCR""]",abstract_body,0.85,frontmatter_main_zone,support_like,none,True,True +1,15,text,"Copyright: © 2022 by the authors. +Licensee MDPI, Basel, Switzerland. +This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) licen","[66.0, 1363.0, 309.0, 1551.0]",frontmatter_noise,0.8,"[""page-1 zone journal_furniture_zone: Copyright: \u00a9 2022 by the authors.\nLicensee MDPI, Basel, Swit""]",frontmatter_noise,0.8,body_zone,body_like,none,False,False +1,16,text,,"[326.0, 901.0, 1124.0, 951.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,frontmatter_main_zone,support_like,empty,True,True +1,17,paragraph_title,1. Introduction,"[329.0, 1028.0, 473.0, 1050.0]",section_heading,0.85,"[""paragraph_title label with numbering: 1. Introduction""]",section_heading,0.85,body_zone,heading_like,heading_numbered,True,True +1,18,text,"Articular cartilage (AC) is a highly complex and specialized connective tissue present in diarthrodial joints and is paramount for joint mobility and health. Regarding cell populations, AC is composed","[325.0, 1056.0, 1125.0, 1538.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,19,footer,"Gels 2022, 8, 710. https://doi.org/10.3390/gels8110710","[67.0, 1625.0, 460.0, 1647.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +1,20,footer,https://www.mdpi.com/journal/gels,"[843.0, 1625.0, 1121.0, 1648.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +2,0,header,"Gels 2022, 8, 710","[67.0, 111.0, 187.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +2,1,header,2 of 18,"[1068.0, 111.0, 1121.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,frontmatter_main_zone,reference_like,reference_numeric_dot,False,False +2,2,text,"AC has a complex, multilayered structure, with each zone having different densities of chondrocytes, ECM composition and organization, and water content. The superficial zone makes up to 10–20% of tot","[324.0, 192.0, 1124.0, 393.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,3,text,"The intrafibrillar water present within the tissue is able to move through the ECM when the tissue experiences compression, despite existing a high frictional resistance to this flow within the tissue","[324.0, 394.0, 1124.0, 669.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,4,text,"Osteoarthritis (OA) is the most common degenerative joint disorder, characterized by a progressive loss of AC and severe joint pain and stiffness $ [10] $. In fact, it is a leading cause of disabilit","[325.0, 670.0, 1124.0, 870.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,5,text,"Pharmaceutical therapy is the most common option for OA treatment, and largely consists of acetaminophen, non-steroidal anti-inflammatory drugs, opioid analgesics, and serotonin-norepinephrine re-upta","[325.0, 870.0, 1124.0, 1096.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,6,text,"Considering the unmet medical need for the effective treatment of OA, cartilage tissue engineering (CTE) has emerged as a promising alternative to treat AC defects [17]. CTE employs the use of a bioco","[325.0, 1097.0, 1124.0, 1347.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,7,text,"Concerning the main cell sources used in CTE strategies, mesenchymal stem/stromal cells (MSCs) have been widely explored as an alternative to chondrocytes due to their ready availability from differen","[325.0, 1347.0, 1125.0, 1549.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,0,header,"Gels 2022, 8, 710","[68.0, 111.0, 187.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +3,1,header,3 of 18,"[1068.0, 111.0, 1121.0, 132.0]",noise,0.9,"[""header label""]",noise,0.9,,reference_like,reference_numeric_dot,False,False +3,2,text,"when compared to MSCs isolated from non-joint tissues [21–23]. Moreover, in recent years, alternative cell sources including articular cartilage progenitor cells (ACPCs) and induced pluripotent stem c","[323.0, 192.0, 1124.0, 293.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,3,text,"Various growth factors and other bioactive molecules have been used as candidates to promote cartilage regeneration. For example, TGF- $ \beta $3 has been demonstrated to enhance the chondrogenesis of","[323.0, 294.0, 1125.0, 619.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,4,text,"Hydrogels are highly absorbent polymer networks swollen in large quantities of water, yet maintaining well-defined structures [30]. Biomedical applications of hydrogels started about 60 years ago, and","[323.0, 620.0, 1125.0, 1324.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,5,text,"Hydrogels for CTE strategies have been fabricated using both natural and synthetic polymers. Hydrogels produced from natural polymers (e.g., alginate, gelatin, collagen, hyaluronic acid, chondroitin s","[324.0, 1323.0, 1125.0, 1526.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,0,header,"Gels 2022, 8, 710","[68.0, 111.0, 187.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +4,1,number,4 of 18,"[1069.0, 111.0, 1121.0, 131.0]",noise,0.9,"[""page number label""]",noise,0.9,,reference_like,reference_numeric_dot,False,False +4,2,text,"mechanical loading), batch-to-batch variability, and difficult processability and control over structural properties and degradation rate [38–40].","[325.0, 192.0, 1123.0, 242.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,3,text,"These extensive customizable features alongside their native-like swelling properties, have allowed the widespread use of hydrogels in CTE strategies [41]. Hydrogels can be designed to be structurally","[324.0, 240.0, 1125.0, 951.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,4,figure_title,Table 1. Examples of hydrogels materials used as injectable systems for CTE applications.,"[327.0, 970.0, 1046.0, 994.0]",table_caption,0.9,"[""table prefix matched: Table 1. Examples of hydrogels materials used as injectable ""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +4,5,table,
Injectable Hydrogel MaterialAdvantagesDisadvantagesRefs
HeparinNaturally occurring negatively charged GAG able to interact with ECM ,"[329.0, 1003.0, 1120.0, 1410.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +5,0,header,"Gels 2022, 8, 710","[68.0, 111.0, 187.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +5,1,number,5 of 18,"[1069.0, 111.0, 1121.0, 132.0]",noise,0.9,"[""page number label""]",noise,0.9,,reference_like,reference_numeric_dot,False,False +5,2,figure_title,Table 1. Cont.,"[329.0, 191.0, 443.0, 214.0]",table_caption,0.9,"[""table prefix matched: Table 1. Cont.""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +5,3,table,
Injectable Hydrogel MaterialAdvantagesDisadvantagesRefs
AlginateFast gelationCost-effectiveNon-immunogenicNon-toxicLack of ,"[329.0, 223.0, 1119.0, 799.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +5,4,text,"One of the abovementioned biophysical cues is electrical stimulation, which has been shown to increase the proliferation of chondrocytes and secretion of ECM molecules, accelerating the repair of cart","[325.0, 830.0, 1125.0, 1081.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,5,text,"In this review, a summary of the conductive biomaterials that have been utilized in conjunction with hydrogels is presented. The current state of development of electrically conductive hydrogels for A","[326.0, 1081.0, 1125.0, 1183.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,0,header,"Gels 2022, 8, 710","[68.0, 111.0, 187.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +6,1,number,6 of 18,"[1069.0, 111.0, 1122.0, 132.0]",noise,0.9,"[""page number label""]",noise,0.9,,reference_like,reference_numeric_dot,False,False +6,2,image,,"[164.0, 184.0, 1023.0, 1031.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,3,figure_title,Figure 1. Electrically conductive hydrogels as a promising tool for the repair of articular cartilage defects caused by trauma or debilitating diseases such as osteoarthritis (top). These functional c,"[325.0, 1054.0, 1123.0, 1133.0]",figure_caption,0.92,"[""figure_title label: Figure 1. Electrically conductive hydrogels as a promising t""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +6,4,paragraph_title,2. Electrical Properties of Articular Cartilage Tissue,"[327.0, 1146.0, 803.0, 1171.0]",section_heading,0.85,"[""paragraph_title label with numbering: 2. Electrical Properties of Articular Cartilage Tissue""]",section_heading,0.85,body_zone,reference_like,reference_numeric_dot,True,True +6,5,text,"AC has intrinsic electrical/electrochemical properties, derived from the flow of free electrolytes (K⁺, Ca²⁺, Na⁺) through the fixed negative charges of carboxyl and sulfate groups attached to the GAG","[325.0, 1178.0, 1125.0, 1455.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,6,paragraph_title,3. Conductive Materials for Tissue Engineering,"[327.0, 1473.0, 768.0, 1498.0]",section_heading,0.85,"[""paragraph_title label with numbering: 3. Conductive Materials for Tissue Engineering""]",section_heading,0.85,body_zone,reference_like,reference_numeric_dot,True,True +6,7,text,A great variety of conductive materials can be implemented with hydrogels in order to create electrically conductive scaffolds. These platforms are invaluable for CTE as they can,"[326.0, 1505.0, 1124.0, 1555.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,0,header,"Gels 2022, 8, 710","[68.0, 111.0, 187.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +7,1,number,7 of 18,"[1068.0, 110.0, 1121.0, 132.0]",noise,0.9,"[""page number label""]",noise,0.9,,reference_like,reference_numeric_dot,False,False +7,2,text,"provide not only native-like physical properties, but are responsive to relevant biophysical cues such as electrical stimulation, simulating a more physiological environment. Despite some combinations","[324.0, 192.0, 1124.0, 368.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,3,paragraph_title,3.1. Metallic Nanoparticles,"[329.0, 387.0, 558.0, 411.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 3.1. Metallic Nanoparticles""]",subsection_heading,0.85,body_zone,heading_like,heading_numbered,True,True +7,4,text,"Metallic nanoparticles are electrically conductive nanosized particles, with a metal core shelled by an inorganic or organic metal or metal oxide, behaving differently according to their size, shape, ","[324.0, 417.0, 1125.0, 1125.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,5,figure_title,Table 2. Properties and applications of metallic nanoparticles.,"[327.0, 1147.0, 824.0, 1171.0]",table_caption,0.9,"[""table prefix matched: Table 2. Properties and applications of metallic nanoparticl""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +7,6,table,
Nanoparticle MaterialAdvantagesDisadvantagesApplicationsReferences
Gold nanoparticles (Au NPs)Low initial cytotoxicityHigh ,"[67.0, 1184.0, 1118.0, 1521.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +8,0,header,"Gels 2022, 8, 710","[68.0, 111.0, 187.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +8,1,number,8 of 18,"[1069.0, 111.0, 1121.0, 131.0]",noise,0.9,"[""page number label""]",noise,0.9,,reference_like,reference_numeric_dot,False,False +8,2,paragraph_title,3.2. Graphene-Based Materials and Carbon Nanotubes,"[327.0, 192.0, 778.0, 217.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 3.2. Graphene-Based Materials and Carbon Nanotubes""]",subsection_heading,0.85,body_zone,heading_like,heading_numbered,True,True +8,3,text,Both graphene and carbon nanotubes (CNTs) are conductive materials with high tensile strengths that can be employed to reinforce and provide conductivity to hydrogel biomatrices with a broad range of ,"[324.0, 223.0, 1125.0, 500.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +8,4,text,"CNTs are cylindrical shaped tubes with nanosized diameters. Due to their high tensile strength, excellent electric and thermal conductivity, their coupling with hydrogel matrices has seen a widespread","[324.0, 499.0, 1126.0, 905.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +8,5,figure_title,Table 3. Properties and applications of graphene and carbon nanotubes.,"[326.0, 927.0, 907.0, 950.0]",table_caption,0.9,"[""table prefix matched: Table 3. Properties and applications of graphene and carbon ""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +8,6,table,"
Carbon TypeAdvantagesDisadvantagesApplicationsReferences
GrapheneHigh mechanical strengthOxidative str","[67.0, 964.0, 1119.0, 1149.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +8,7,paragraph_title,3.3. Conductive Polymers,"[328.0, 1180.0, 546.0, 1205.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 3.3. Conductive Polymers""]",subsection_heading,0.85,body_zone,heading_like,heading_numbered,True,True +8,8,text,Conductive polymers are organic polymers with unique mechanical and optical properties. They have characteristics similar to some metals and inorganic semiconductors while maintaining characteristic p,"[324.0, 1210.0, 1127.0, 1566.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,0,header,"Gels 2022, 8, 710","[67.0, 111.0, 187.0, 132.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +9,1,number,9 of 18,"[1068.0, 111.0, 1122.0, 131.0]",noise,0.9,"[""page number label""]",noise,0.9,,reference_like,reference_numeric_dot,False,False +9,2,text,gies both as coating material and mixed with other biomaterials [123–126]. Our group has recently showed that PEDOT:PSS coated polybenzimidazole nanofibers were able to promote the adhesion and prolif,"[324.0, 192.0, 1126.0, 446.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,3,figure_title,Table 4. Properties and applications of main conductive polymers.,"[326.0, 467.0, 863.0, 491.0]",table_caption,0.9,"[""table prefix matched: Table 4. Properties and applications of main conductive poly""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +9,4,table,,"[68.0, 506.0, 1119.0, 805.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +9,5,paragraph_title,4. Electrically Conductive Hydrogels for Articular Cartilage Tissue Engineering,"[327.0, 835.0, 1059.0, 860.0]",section_heading,0.85,"[""paragraph_title label with numbering: 4. Electrically Conductive Hydrogels for Articular Cartilage""]",section_heading,0.85,body_zone,reference_like,reference_numeric_dot,True,True +9,6,text,"The fabrication of hydrogels with different materials and properties as cartilage-healing constructs is well documented. However, recently there has been an emergence of a few research studies trying ","[323.0, 866.0, 1125.0, 1092.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,7,text,"The underlying mechanisms through which endogenous or external electrical stimuli influence cell behavior are still poorly described. However, the alteration of cell membrane resting potential by elec","[324.0, 1093.0, 1126.0, 1494.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,8,text,"When designing conductive hydrogel scaffolds as cartilage substitutes, some parameters are necessary to consider in order to correctly recapitulating the native environment, including the mechanical s","[326.0, 1495.0, 1127.0, 1572.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,0,header,"Gels 2022, 8, 710","[68.0, 111.0, 187.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +10,1,header,10 of 18,"[1062.0, 111.0, 1122.0, 132.0]",noise,0.9,"[""header label""]",noise,0.9,,reference_like,reference_numeric_dot,False,False +10,2,text,"ibility. Despite literature on this topic being scarce, the existing results are highly promising, highlighting the potential of electrically conductive hydrogels for improved CTE strategies (Table 5)","[325.0, 192.0, 1123.0, 266.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,3,text,"Zhang et al., produced a poly(vinyl alcohol) (PVA) hydrogel combined with sodium phytate (PANa), which conferred conductivity and excellent mechanical properties to the hydrogel [141]. The mechanical ","[323.0, 269.0, 1124.0, 645.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,4,text,"In a different study, Shen and colleagues investigated the chondrogenic inducing potential of a graphene oxide (GO) containing poly-D,L-lactic acid/polyethylene glycol (PDLLA) nanocomposite hydrogel [","[325.0, 644.0, 1124.0, 1071.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +10,5,text,3D printing allows layer-by-layer development of 3D structures and the fabrication of complex scaffolds in a fast and reproducible manner. Given that this technique enables a precise control over the ,"[325.0, 1071.0, 1126.0, 1525.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +11,0,header,"Gels 2022, 8, 710","[67.0, 111.0, 187.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +11,1,header,11 of 18,"[1061.0, 111.0, 1122.0, 132.0]",noise,0.9,"[""header label""]",noise,0.9,,reference_like,reference_numeric_dot,False,False +11,2,figure_title,Table 5. Summary of research studies on electrically conductive hydrogels for AC tissue engineering.,"[326.0, 192.0, 1122.0, 216.0]",table_caption,0.9,"[""table prefix matched: Table 5. Summary of research studies on electrically conduct""]",table_caption,0.9,display_zone,table_caption_like,table_number,True,True +11,3,table,
Conductive Polymer TypeAdvantagesDisadvantagesApplicationsReferences
Polyaniline (PANi)High stabilityHigh conductivity
HydrogelConductive FillerMain OutcomesReferences
Poly(vinyl alcohol) (PVA)Sodium phytate (PANa)Easy to produce and cost-eff,"[328.0, 223.0, 1119.0, 844.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,body_zone,body_like,none,True,True +11,4,paragraph_title,5. Challenges and Future Perspectives,"[328.0, 874.0, 683.0, 897.0]",section_heading,0.85,"[""paragraph_title label with numbering: 5. Challenges and Future Perspectives""]",section_heading,0.85,body_zone,reference_like,reference_numeric_dot,True,True +11,5,text,The promising results observed in the few studies developing electrically conductive hydrogels for AC regeneration highlight its potential as a suitable culture platform for improved CTE strategies. H,"[324.0, 903.0, 1125.0, 1382.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +11,6,text,"Another challenge limiting the application of conductive hydrogels in regenerative medicine is their low processability by 3D additive manufacturing techniques. In fact, the fabrication of complex str","[325.0, 1381.0, 1126.0, 1535.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +12,0,header,"Gels 2022, 8, 710","[68.0, 111.0, 187.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +12,1,number,12 of 18,"[1062.0, 111.0, 1122.0, 132.0]",noise,0.9,"[""page number label""]",noise,0.9,,reference_like,reference_numeric_dot,False,False +12,2,text,structures should be explored with high potential for introducing major advances in AC and osteochondral tissue engineering.,"[326.0, 192.0, 1122.0, 241.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +12,3,text,"Furthermore, a deeper understanding of the tissue's electrical properties is necessary in order to successfully mimic the AC's native niche and achieve proper regeneration outcomes. Novel methods to d","[325.0, 243.0, 1125.0, 721.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +12,4,paragraph_title,6. Conclusions,"[329.0, 740.0, 471.0, 763.0]",section_heading,0.85,"[""paragraph_title label with numbering: 6. Conclusions""]",section_heading,0.85,body_zone,heading_like,heading_numbered,True,True +12,5,text,"CTE has emerged as an exciting alternative to the current ineffective treatments for cartilage damage and degeneration, as in cases of OA. In particular, the development of electrically conductive hyd","[326.0, 770.0, 1124.0, 895.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +12,6,text,"In summary, this review provides an overview of the most common conductive materials that have been combined with hydrogels for tissue engineering and other biomedical applications. Conductive materia","[325.0, 896.0, 1125.0, 1201.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +12,7,text,"Author Contributions: Conceptualization: F.M., F.C.F. and J.C.S.; investigation: F.M. and J.C.S.; writing—original draft preparation: F.M., F.B. and J.C.S.; writing—review and editing: F.M., F.B., F.C","[326.0, 1220.0, 1124.0, 1316.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,support_like,none,True,True +12,8,text,"Funding: The authors acknowledge funding from FCT—Portuguese Foundation for Science and Technology (FCT/MCTES), with dedicated funding from InSilico4OCReg (PTDC/EME-SIS/0838/2021) and OptiBioScaffold ","[326.0, 1326.0, 1124.0, 1444.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +12,9,text,Data Availability Statement: Not applicable.,"[328.0, 1454.0, 696.0, 1479.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +12,10,text,Conflicts of Interest: The authors declare no conflict of interest.,"[328.0, 1490.0, 840.0, 1513.0]",frontmatter_noise,0.88,"[""default body_paragraph for text label"", ""late role resolution: editorial phrase cross-validates non-body classification"", ""zone=body_zone"", ""style_family=support_like""]",body_paragraph,0.6,body_zone,support_like,none,False,False +13,0,header,"Gels 2022, 8, 710","[67.0, 111.0, 187.0, 131.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +13,1,number,13 of 18,"[1061.0, 111.0, 1122.0, 131.0]",reference_item,0.9,"[""page number label""]",noise,0.9,reference_zone,reference_like,reference_numeric_dot,True,True +13,2,paragraph_title,References,"[67.0, 192.0, 176.0, 215.0]",reference_heading,0.9,"[""references heading: References""]",reference_heading,0.9,reference_zone,heading_like,short_fragment,True,True +13,3,reference_content,"1. 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Black-Phosphorus-Incorporated Hydrogel as a Conductive and Biodegradable Platform for Enhancement of the Neural Differenti","[68.0, 609.0, 1123.0, 673.0]",reference_item,0.85,"[""reference content label: 148. Xu, C.; Xu, Y.; Yang, M.; Chang, Y.; Nie, A.; Liu, Z.; ""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +18,12,reference_content,"149. Da Silva, L.P.; Kundu, S.C.; Reis, R.L.; Correlo, V.M. Electric Phenomenon: A Disregarded Tool in Tissue Engineering and Regenerative Medicine. Trends Biotechnol. 2020, 38, 24–49. [CrossRef]","[68.0, 677.0, 1120.0, 721.0]",reference_item,0.85,"[""reference content label: 149. Da Silva, L.P.; Kundu, S.C.; Reis, R.L.; Correlo, V.M. ""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +18,13,reference_content,"150. Bansal, M.; Dravid, A.; Aqrawe, Z.; Montgomery, J.; Wu, Z.; Svirskis, D. Conducting polymer hydrogels for electrically responsive drug delivery. J. Control. Release 2020, 328, 192–209. [CrossRef]","[71.0, 722.0, 1120.0, 767.0]",reference_item,0.85,"[""reference content label: 150. Bansal, M.; Dravid, A.; Aqrawe, Z.; Montgomery, J.; Wu,""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +18,14,reference_content,"151. Gelmi, A.; Schutt, C.E. Stimuli-Responsive Biomaterials: Scaffolds for Stem Cell Control. Adv. Healthc. Mater. 2021, 10, 2001125. [CrossRef] [PubMed]","[70.0, 769.0, 1121.0, 813.0]",reference_item,0.85,"[""reference content label: 151. Gelmi, A.; Schutt, C.E. Stimuli-Responsive Biomaterials""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +18,15,reference_content,"152. Maeng, W.-Y.; Tseng, W.-L.; Li, S.; Koo, J.; Hsueh, Y.-Y. Electrocuticals for peripheral nerve regeneration. Biofabrication 2022, 14, 42002. [CrossRef] [PubMed]","[68.0, 816.0, 1123.0, 858.0]",reference_item,0.85,"[""reference content label: 152. 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Conclusions", + "found_in_fulltext": true, + "fulltext_offset": 36579 + }, + { + "block_id": "p12:5", + "page": 12, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "CTE has emerged as an exciting alternative to the current ineffective treatments", + "found_in_fulltext": true, + "fulltext_offset": 36594 + }, + { + "block_id": "p12:6", + "page": 12, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "In summary, this review provides an overview of the most common conductive mater", + "found_in_fulltext": true, + "fulltext_offset": 37039 + }, + { + "block_id": "p12:7", + "page": 12, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Author Contributions: Conceptualization: F.M., F.C.F. and J.C.S.; investigation:", + "found_in_fulltext": true, + "fulltext_offset": 38111 + }, + { + "block_id": "p12:8", + "page": 12, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Funding: The authors acknowledge funding from FCT—Portuguese Foundation for Scie", + "found_in_fulltext": true, + "fulltext_offset": 38475 + }, + { + "block_id": "p12:9", + "page": 12, + "role": "body_paragraph", + "zone": "body_zone", + "render_default": true, + "snippet": "Data Availability Statement: Not applicable.", + "found_in_fulltext": true, + "fulltext_offset": 38860 + }, + { + "block_id": "p13:0", + "page": 13, + "role": "noise", + "zone": "body_zone", + "render_default": false, + "snippet": "Gels 2022, 8, 710", + "found_in_fulltext": false, + "fulltext_offset": -1 + }, + { + "block_id": "p13:1", + "page": 13, + "role": "reference_item", + "zone": "reference_zone", + "render_default": true, + "snippet": "13 of 18", + "found_in_fulltext": true, + "fulltext_offset": 38922 + }, + { + "block_id": "p13:2", + "page": 13, + "role": "reference_heading", + "zone": "reference_zone", + "render_default": true, + "snippet": "References", + "found_in_fulltext": true, + "fulltext_offset": 38934 + }, + { + "block_id": "p13:3", + "page": 13, + "role": "reference_item", + "zone": "reference_zone", + "render_default": true, + "snippet": "1. 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"p7:12" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p7:13" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p7:14" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p7:15" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p7:16" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p7:17" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p7:18" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p7:19" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p7:20" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p7:21" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p7:22" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p8:0" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_008.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p8:1" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_008.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p8:2" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_008.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p8:3" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_008.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p8:4" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_008.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p8:5" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_008.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p8:6" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_008.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p8:7" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_008.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "reference_span_error", + "severity": "critical", + "block_ids": [ + "p8:8" + ], + "truth": "block should remain outside the accepted reference span", + "pipeline_behavior": "block appears inside the logical reference reading-order region", + "root_cause_hypothesis": "logical_order_between_reference_members", + "evidence": { + "annotated_page": "annotated_pages/page_008.png", + "artifact": "reference_span_audit.json" + } + }, + { + "category": "same_page_boundary_error", + "severity": "major", + "block_ids": [], + "truth": "body/reference/backmatter boundaries should be explainable at block level", + "pipeline_behavior": "page contains mixed body/reference/tail signals", + "root_cause_hypothesis": "same-page boundary ambiguity", + "evidence": { + "annotated_page": "annotated_pages/page_007.png", + "artifact": "page_risk_summary.json" + } + }, + { + "category": "render_mapping_error", + "severity": "minor", + "block_ids": [ + "p1:0", + "p1:3", + "p1:11", + "p1:12", + "p2:0", + "p3:1", + "p3:13", + "p4:0", + "p4:10", + "p5:1", + "p5:4", + "p6:0", + "p6:1", + "p6:6", + "p7:0", + "p7:1", + "p8:0" + ], + "truth": "rendered fulltext should be traceable back to source blocks", + "pipeline_behavior": "some render-default blocks are not easily mapped into the current fulltext output", + "root_cause_hypothesis": "render omission or snippet mismatch", + "evidence": { + "annotated_page": null, + "artifact": "fulltext_block_mapping_summary.json" + } + } + ] +} \ No newline at end of file diff --git a/audit/72D4YXEB/audit_report.md b/audit/72D4YXEB/audit_report.md new file mode 100644 index 00000000..6194b8bd --- /dev/null +++ b/audit/72D4YXEB/audit_report.md @@ -0,0 +1,37 @@ +# OCR Truth Audit Report - 72D4YXEB + +- Mode: `high-risk` +- Status: `READY` +- Reviewed pages: [1, 2, 3, 4, 5, 6, 7] +- Reviewed blocks: 92 + +## Findings + +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `critical` `reference_span_error`: block appears inside the logical reference reading-order region +- `major` `same_page_boundary_error`: page contains mixed body/reference/tail signals +- `minor` `render_mapping_error`: some render-default blocks are not easily mapped into the current fulltext output + +## Disposition Guidance + +- Use `repair` when the finding reflects a pipeline defect worth fixing now. +- Use `residual` when the finding is real but intentionally deferred. +- Do not rewrite expected truth to make current output look correct. diff --git a/audit/72D4YXEB/audit_scope.json b/audit/72D4YXEB/audit_scope.json new file mode 100644 index 00000000..614462fb --- /dev/null +++ b/audit/72D4YXEB/audit_scope.json @@ -0,0 +1,614 @@ +{ + "mode": "high-risk", + "selected_pages": [ + 1, + 2, + 3, + 4, + 5, + 6, + 7 + ], + "required_block_ids": [ + "p1:0", + "p1:1", + "p1:2", + "p1:3", + "p1:4", + "p1:5", + "p1:6", + "p1:7", + "p1:8", + "p1:9", + "p1:10", + "p1:11", + "p1:12", + "p2:2", + "p3:2", + "p4:2", + "p5:2", + "p6:2", + "p6:3", + "p6:4", + "p7:2", + "p7:3", + "p7:4", + "p7:8", + "p7:12", + "p7:13", + "p7:14", + "p7:15", + "p7:16", + "p7:17", + "p7:18", + "p7:19", + "p7:20", + "p7:21", + "p7:22" + ], + "required_blocks": [ + { + "block_id": "p1:0", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:1", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:2", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:3", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:4", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:5", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:6", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:7", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:8", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:9", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + "review_status", + "truth_role", + "truth_zone", + "truth_reference_membership" + ] + }, + { + "block_id": "p1:10", + "page": 1, + "required_reason": [ + "frontmatter" + ], + "minimum_fields": [ + "block_id", + "page", + 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Cartila""]",paper_title,0.8,frontmatter_main_zone,support_like,none,True,True +1,2,text,"Cartilage +2016, Vol. 7(1) 62–69 +© The Author(s) 2015 +Reprints and permissions: +sagepub.com/journalsPermissions.nav +DOI: 10.1177/1947603515599191 +cart.sagepub.com +SAGE","[858.0, 119.0, 1079.0, 268.0]",frontmatter_noise,0.8,"[""page-1 zone journal_furniture_zone: Cartilage\n2016, Vol. 7(1) 62\u201369\n\u00a9 The Author(s) 2015\nReprint""]",frontmatter_noise,0.8,frontmatter_main_zone,support_like,none,False,False +1,3,text,"Christoph Becher $ ^{1} $, Marcel Ricklefs $ ^{1} $, Elmar Willbold $ ^{2} $, Christof Hurschler $ ^{2} $, and Reza Abedian $ ^{2} $","[89.0, 325.0, 927.0, 384.0]",authors,0.8,"[""page-1 zone author_zone: Christoph Becher $ ^{1} $, Marcel Ricklefs $ ^{1} $, Elmar W""]",authors,0.8,frontmatter_main_zone,support_like,none,True,True +1,4,paragraph_title,Abstract,"[91.0, 454.0, 183.0, 477.0]",abstract_heading,0.95,"[""abstract heading""]",abstract_heading,0.95,frontmatter_main_zone,heading_like,short_fragment,True,True +1,5,abstract,Purpose: To assess the electromechanical properties of human knee articular cartilage with compression-induced streaming potentials for reliability among users and correlation with macroscopic and his,"[87.0, 479.0, 1085.0, 842.0]",abstract_body,0.85,"[""abstract label from Paddle OCR""]",abstract_body,0.85,frontmatter_main_zone,support_like,none,True,True +1,6,paragraph_title,Keywords,"[91.0, 873.0, 193.0, 896.0]",structured_insert,0.9,"[""frontmatter noise: Keywords""]",frontmatter_noise,0.9,frontmatter_main_zone,heading_like,short_fragment,False,False +1,7,text,"streaming potential integrals (SPI), articular cartilage, osteoarthritis, ICRS/Mankin score","[90.0, 898.0, 805.0, 923.0]",frontmatter_noise,0.7,"[""keyword-like block: streaming potential integrals (SPI), articular cartilage, os""]",frontmatter_noise,0.7,frontmatter_main_zone,support_like,none,False,False +1,8,paragraph_title,Introduction,"[92.0, 983.0, 241.0, 1007.0]",section_heading,0.9,"[""explicit scholarly heading: Introduction""]",section_heading,0.9,body_zone,heading_like,canonical_section_name,True,True +1,9,text,"Articular cartilage defects are common findings at arthroscopic surgery of the knee joint. $ ^{1-3} $ These defects may be the cause of a variety of symptoms, such as swelling, pain, or joint stiffnes","[89.0, 1021.0, 575.0, 1431.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,10,text,,"[598.0, 982.0, 1085.0, 1177.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,frontmatter_main_zone,support_like,empty,True,True +1,11,footnote," $ ^{1} $Department of Orthopedic Surgery, Hannover Medical School, Hannover, Germany + $ ^{2} $Laboratory for Biomechanics and Biomaterials, Hannover Medical School, Hannover, Germany","[600.0, 1233.0, 1042.0, 1316.0]",footnote,0.7,"[""footnote label: $ ^{1} $Department of Orthopedic Surgery, Hannover Medical S""]",footnote,0.7,body_zone,body_like,affiliation_marker,True,True +1,12,footnote,"Corresponding Author: +Christoph Becher, Department of Orthopedic Surgery, Hannover Medical School, 1-7 Anna-von-Borries-Straße, 30625 Hannover, Germany. +Email: becher.chris@web.de","[599.0, 1325.0, 1039.0, 1428.0]",frontmatter_support,0.75,"[""page-1 correspondence footnote: Corresponding Author:\nChristoph Becher, Department of Orthop""]",frontmatter_support,0.75,body_zone,body_like,none,True,True +2,0,header,Becher et al.,"[123.0, 81.0, 223.0, 103.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +2,1,number,63,"[1087.0, 81.0, 1112.0, 102.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +2,2,image,,"[307.0, 151.0, 932.0, 418.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +2,3,figure_title,Figure 1. (a) Principle of the technique for the measurement of compression-induced streaming potentials of articular cartilage according to the user manual. $ ^{16} $ As a result of compression loadi,"[120.0, 449.0, 1107.0, 558.0]",figure_caption,0.92,"[""figure_title label: Figure 1. (a) Principle of the technique for the measurement""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +2,4,text,"and healing grafts, more reliable and sensitive measurement techniques are necessary.","[119.0, 594.0, 603.0, 640.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,5,text,"In recent years, several diagnostic tools capable of objective evaluation of the cartilage properties in the early and potentially reversible stages of the disease have been developed to assess the st","[120.0, 641.0, 605.0, 1026.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,6,text,The device investigated herein relies on the fact that streaming potentials are induced in cartilage in response to loading. The extracellular matrix is loaded with negatively charged proteoglycans th,"[119.0, 1026.0, 606.0, 1435.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,7,text,,"[628.0, 592.0, 1114.0, 906.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +2,8,text,"In this study, multiuser repeating measurements were performed to assess the learning phase for different users in 10 human knee cadaver specimens in vitro and under benchtop measurement configuration","[628.0, 907.0, 1115.0, 1171.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,9,paragraph_title,Materials and Methods Specimen Preparation and SPI Measurements,"[629.0, 1211.0, 1052.0, 1278.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Materials and Methods Specimen Preparation and SPI Measureme""]",subsection_heading,0.6,body_zone,heading_like,none,True,True +2,10,footer,,"[629.0, 1251.0, 1052.0, 1278.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,empty,False,False +2,11,text,"After approval of the local ethics committee (IRB No. 1182-2011), femoral condyles of 10 fresh human cadaver knee specimen (2 male, 3 female, mean age 58 [43-65] years) were dissected and distal femur","[628.0, 1288.0, 1115.0, 1435.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,0,number,64,"[93.0, 81.0, 120.0, 102.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +3,1,header,Cartilage 7(1),"[972.0, 80.0, 1083.0, 104.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +3,2,image,,"[240.0, 158.0, 921.0, 383.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +3,3,figure_title,"Figure 2. (a) Location scheme for distal femur with measurement points marked on the anatomical locations for SPI measurement (L, lateral; M, medial). (b) Tip of the Arthro-BST hemispherical indentati","[90.0, 414.0, 1066.0, 481.0]",figure_caption,0.92,"[""figure_title label: Figure 2. (a) Location scheme for distal femur with measurem""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +3,4,text,ink-marked on the trochlea (2-3) and medial/lateral condyles (14) according to a standardized location scheme (Fig. 2). The thus defined measurement locations were evaluated by an experienced board-ce,"[89.0, 514.0, 575.0, 779.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,5,text,The testing chamber was filled with phosphate-buffered saline (pH 7.4) and a minimum of 15 minutes was allowed for equilibration prior to electromechanical mapping. Streaming potentials were measured ,"[88.0, 779.0, 576.0, 1116.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,6,paragraph_title,Histological and Biochemical Evaluation,"[91.0, 1148.0, 454.0, 1175.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Histological and Biochemical Evaluation""]",subsection_heading,0.6,body_zone,heading_like,none,True,True +3,7,text,"A total of 162 equal osteochondral cylinders of 6-mm diameter and 8-mm height were harvested from the marked locations with orthopedic tissue punches (Osteochondral Autograft Transfer System [OATS], A","[89.0, 1186.0, 574.0, 1356.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,8,text,"General Histology. The cylinders were first fixed in commercial 3.5% formalin for 5 days at room temperature. Then, the cylinders were washed, dehydrated in a graded series of ethanol, embedded in met","[89.0, 1378.0, 575.0, 1452.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,9,text,,"[599.0, 514.0, 1085.0, 756.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +3,10,text,"Hematoxylin–Eosin Staining. Rehydrated sections were first rinsed in distilled water for 2 minutes, then stained for 6 minutes with Mayer's hematoxylin (Merck), rinsed in tap water for 10 minutes, the","[599.0, 778.0, 1085.0, 924.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,11,text,"Safranin-O Staining. Rehydrated sections were incubated for 4 minutes in a solution of 0.1% safranin-O (Sigma, Taufkirchen, Germany), then washed in distilled water, dehydrated in a graded series of e","[599.0, 945.0, 1085.0, 1044.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,12,text,"Mankin Score. Mankin scores were determined for the histological evaluation. Values range from 0 (healthy cartilage) to 14 (severe cartilage destruction), distributed in 4 categories: structure (range","[600.0, 1066.0, 1084.0, 1284.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,13,text,"Biochemical Evaluation. The content of sGAG (reported in $ \mu $g/mL, normalized to a standardized sample surface area of 28.3 mm $ ^{2} $) was determined using the commercially available Blyscan Ass","[599.0, 1305.0, 1086.0, 1452.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,0,header,Becher et al.,"[123.0, 81.0, 223.0, 103.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +4,1,number,65,"[1087.0, 81.0, 1113.0, 102.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +4,2,chart,,"[302.0, 150.0, 934.0, 633.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,3,figure_title,Figure 3. Box plots displaying the SPI measurements of the 3 observers. The interclass correlation coefficient (ICC) was 0.77 (0.70-0.83) indicating good to excellent linear agreement of streaming pot,"[120.0, 659.0, 1102.0, 706.0]",figure_caption,0.92,"[""figure_title label: Figure 3. Box plots displaying the SPI measurements of the 3""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +4,4,text,"the cartilage cylinders, each specimen was dissolved in 1.5-mL microcentrifuge tubes in a papain extraction reagent, containing 100 mL of 0.2 M sodium phosphate buffer (pH 6.4) with 0.82 g of sodium a","[119.0, 739.0, 605.0, 1245.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,5,paragraph_title,Data Evaluation and Statistical Methods,"[121.0, 1278.0, 492.0, 1303.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Data Evaluation and Statistical Methods""]",subsection_heading,0.6,body_zone,heading_like,none,True,True +4,6,text,"To validate the methodologies of the measurements, 3 of the authors (observer 1, board-certified orthopedic surgeon; observer 2, engineering student trained in the use of the device $ ^{17} $; observe","[119.0, 1316.0, 605.0, 1438.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,7,text,,"[626.0, 739.0, 1115.0, 1054.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +4,8,paragraph_title,Results,"[631.0, 1085.0, 720.0, 1111.0]",section_heading,0.9,"[""explicit scholarly heading: Results""]",section_heading,0.9,body_zone,heading_like,canonical_section_name,True,True +4,9,text,"The computed ICC was 0.77 (0.70-0.83), indicating good to excellent linear agreement of SPI values among the 3 users (Fig. 3). However, unsuccessful measurements occurred at several locations for all ","[628.0, 1123.0, 1113.0, 1340.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +4,10,text,"The mean ICRS score was $ 0.8 \pm 0.7 $ (range 0-3), and the mean Mankin score was $ 2.8 \pm 1.5 $ (range 0-7). Significant negative correlations between SPI and both ICRS and Mankin scores were obs","[628.0, 1341.0, 1115.0, 1437.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,0,number,66,"[94.0, 81.0, 119.0, 102.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +5,1,header,Cartilage 7(1),"[972.0, 80.0, 1083.0, 105.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +5,2,chart,,"[274.0, 149.0, 906.0, 752.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +5,3,figure_title,Figure 4. Linear regression between learning index and number of evaluated knees.,"[90.0, 785.0, 720.0, 807.0]",figure_caption,0.92,"[""figure_title label: Figure 4. Linear regression between learning index and numbe""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +5,4,text,"$r = 0.255$, $P = 0.02$, respectively; Fig. 5a and b) together with a significant positive linear correlation between the ICRS and Mankin scores ($r = 0.334$, $P = 0.002$). No significant correlations","[90.0, 845.0, 574.0, 967.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,5,paragraph_title,Discussion,"[92.0, 999.0, 216.0, 1024.0]",section_heading,0.9,"[""explicit scholarly heading: Discussion""]",section_heading,0.9,body_zone,heading_like,canonical_section_name,True,True +5,6,text,The purpose of this study was to assess the electromechanical properties of human knee articular cartilage with compression-induced streaming potentials for reliability among users and correlation wit,"[89.0, 1037.0, 574.0, 1348.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,7,text,"Standardized methods for evaluating of cartilage defects, cartilage repair tissue, and clinical outcomes of cartilage resurfacing are crucial in both the clinical and research contexts. However, the d","[89.0, 1350.0, 574.0, 1422.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,8,text,,"[598.0, 846.0, 1086.0, 1424.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +6,0,header,Becher et al.,"[123.0, 81.0, 223.0, 103.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +6,1,number,67,"[1087.0, 81.0, 1113.0, 102.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +6,2,chart,,"[138.0, 163.0, 621.0, 543.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,3,chart,,"[626.0, 164.0, 1087.0, 534.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,4,chart,,"[390.0, 554.0, 850.0, 921.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,5,figure_title,"Figure 5. Correlations between streaming potential integral (SPI) values and (a) International Cartilage Repair Society (ICRS) score, (b) Mankin score, and (c) sulfated glycosaminoglycan (sGAG) conten","[120.0, 966.0, 1102.0, 1012.0]",figure_caption,0.92,"[""figure_title label: Figure 5. Correlations between streaming potential integral ""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +6,6,text,"from one pilot study from our group published by Abedian et al. $ ^{17} $, the available literature about the Arthro-BST is somewhat related to the inventers of the device. $ ^{10,14,18-20} $","[120.0, 1046.0, 604.0, 1116.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,7,text,"In the present study, we demonstrated good to excellent linear agreement of SPI values with an ICC of 0.77 (0.70-0.83), which confirms the reliability of the streaming potential measurements among dif","[119.0, 1119.0, 605.0, 1433.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +6,8,text,,"[628.0, 1045.0, 1115.0, 1262.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +6,9,text,"The present study revealed statistically significant negative correlations between SPI and both ICRS (r = 0.502) and Mankin scores (r = 0.255). Although the correlation coefficient was not high, these","[629.0, 1263.0, 1115.0, 1432.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,0,number,68,"[93.0, 81.0, 120.0, 102.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +7,1,header,Cartilage 7(1),"[972.0, 80.0, 1083.0, 105.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +7,2,text,demonstrated comparable findings when correlating the characteristic value (CV) calculated from NIR with a handheld probe to ICRS scores (r = 0.47) $ ^{29} $ and Mankin score (r = 0.55). $ ^{30} $ A g,"[89.0, 134.0, 575.0, 710.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,True,True +7,3,text,"Although the decrease of glycosaminoglycan content is typical for severe cartilage lesions, $ ^{31,32} $ we could not detect a correlation of SPI values to the sGAG content per wet weight. This observ","[89.0, 712.0, 576.0, 1165.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,True,True +7,4,text,"In conclusion, the findings of this study confirm the agreement between the SPI and clinically relevant cartilage scores ex vivo under benchtop conditions substantiating that the SPI values may be use","[89.0, 1167.0, 575.0, 1433.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,body_like,none,True,True +7,5,text,,"[599.0, 134.0, 1085.0, 232.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +7,6,paragraph_title,Acknowledgment and Funding,"[600.0, 259.0, 895.0, 282.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Acknowledgment and Funding""]",subsection_heading,0.6,body_zone,heading_like,none,True,True +7,7,text,"The author(s) received no financial support for the research, authorship, and/or publication of this article.","[599.0, 290.0, 1083.0, 336.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,8,paragraph_title,Declaration of Conflicting Interests,"[601.0, 362.0, 940.0, 386.0]",backmatter_boundary_candidate,0.5,"[""backmatter boundary candidate: Declaration of Conflicting Interests""]",backmatter_boundary_candidate,0.5,body_zone,heading_like,none,True,True +7,9,text,"The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.","[599.0, 393.0, 1084.0, 460.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,10,paragraph_title,Ethical Approval,"[601.0, 486.0, 766.0, 510.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Ethical Approval""]",subsection_heading,0.6,body_zone,heading_like,short_fragment,True,True +7,11,text,The local ethics committee provide ethical approval (IRB No. 1182-2011).,"[600.0, 518.0, 1082.0, 561.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,12,paragraph_title,References,"[602.0, 586.0, 713.0, 609.0]",reference_heading,0.9,"[""references heading: References""]",reference_heading,0.9,reference_zone,heading_like,short_fragment,True,True +7,13,reference_content,"1. 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J Orthop Res. 2002;20(4):819-26.","[123.0, 884.0, 602.0, 967.0]",reference_item,0.85,"[""reference content label: 20. Legare A, Garon M, Guardo R, Savard P, Poole AR, Buschma""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,12,reference_content,21. Mankin HJ. Biochemical and metabolic aspects of osteoarthritis. Orthop Clin North Am. 1971;2(1):19-31.,"[123.0, 971.0, 601.0, 1012.0]",reference_item,0.85,"[""reference content label: 21. Mankin HJ. Biochemical and metabolic aspects of osteoart""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,13,reference_content,"22. Willbold E, Witte F. Histology and research at the hard tissue-implant interface using Technovit 9100 New embedding technique. Acta Biomater. 2010;6(11):4447-55.","[124.0, 1016.0, 602.0, 1079.0]",reference_item,0.85,"[""reference content label: 22. Willbold E, Witte F. Histology and research at the hard ""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,14,reference_content,"23. Brismar BH, Wredmark T, Movin T, Leandersson J, Svensson O. Observer reliability in the arthroscopic classification of","[123.0, 1082.0, 605.0, 1122.0]",reference_item,0.85,"[""reference content label: 23. Brismar BH, Wredmark T, Movin T, Leandersson J, Svensson""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,15,reference_content,osteoarthritis of the knee. J Bone Joint Surg Br. 2002;84(1):42-7.,"[662.0, 135.0, 1110.0, 175.0]",reference_item,0.85,"[""reference content label: osteoarthritis of the knee. J Bone Joint Surg Br. 2002;84(1)""]",reference_item,0.85,reference_zone,unknown_like,none,True,True +8,16,reference_content,"24. Hunt N, Sanchez-Ballester J, Pandit R, Thomas R, Strachan R. Chondral lesions of the knee: a new localization method and correlation with associated pathology. Arthroscopy. 2001;17(5):481-90.","[634.0, 179.0, 1112.0, 264.0]",reference_item,0.85,"[""reference content label: 24. Hunt N, Sanchez-Ballester J, Pandit R, Thomas R, Stracha""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,17,reference_content,"25. Javed A, Siddique M, Vaghela M, Hui AC. Interobserver variations in intra-articular evaluation during arthroscopy of the knee. J Bone Joint Surg Br. 2002;84(1):48-9.","[634.0, 267.0, 1114.0, 330.0]",reference_item,0.85,"[""reference content label: 25. Javed A, Siddique M, Vaghela M, Hui AC. Interobserver va""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,18,reference_content,"26. Jerosch J, Castro WH, de Waal Malefijt MC, Busch M, van Kampen A. Interobserver variation in diagnostic arthroscopy of the knee joint. “How really objective are arthroscopic findings?” Unfallchiru","[634.0, 333.0, 1112.0, 419.0]",reference_item,0.85,"[""reference content label: 26. Jerosch J, Castro WH, de Waal Malefijt MC, Busch M, van ""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,19,reference_content,"27. Garon M, Legare A, Quenneville E, Sims TJ, Hurtig MB, Shive MS, et al. Arthroscopic device measuring streaming potentials reliably indicates functional properties of cartilage. Osteoarthritis Cart","[634.0, 421.0, 1111.0, 507.0]",reference_item,0.85,"[""reference content label: 27. Garon M, Legare A, Quenneville E, Sims TJ, Hurtig MB, Sh""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,20,reference_content,"28. Changoor A, Quenneville E, Garon M, Cloutier L, Hurtig MB, Buschmann MD. Streaming potential-based arthroscopic device discerns topographical differences in cartilage covered and uncovered by meni","[634.0, 509.0, 1112.0, 616.0]",reference_item,0.85,"[""reference content label: 28. Changoor A, Quenneville E, Garon M, Cloutier L, Hurtig M""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,21,reference_content,"29. Marticke JK, Hosselbarth A, Hoffmeier KL, Marintschev I, Otto S, Lange M, et al. How do visual, spectroscopic and biomechanical changes of cartilage correlate in osteoarthritic knee joints? Clin B","[634.0, 620.0, 1112.0, 704.0]",reference_item,0.85,"[""reference content label: 29. Marticke JK, Hosselbarth A, Hoffmeier KL, Marintschev I,""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,22,reference_content,"30. Pester JK, Stumpfe ST, Steinert S, Marintschev I, Plettenberg HK, Aurich M, et al. Histological, biochemical and spectroscopic changes of articular cartilage in osteoarthritis: is there a chance f","[634.0, 708.0, 1112.0, 814.0]",reference_item,0.85,"[""reference content label: 30. Pester JK, Stumpfe ST, Steinert S, Marintschev I, Plette""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,23,reference_content,"31. Bonassar LJ, Jeffries KA, Paguio CG, Grodzinsky AJ. Cartilage degradation and associated changes in biochemical and electromechanical properties. Acta Orthop Scand Suppl. 1995;266:38-44.","[634.0, 818.0, 1111.0, 901.0]",reference_item,0.85,"[""reference content label: 31. Bonassar LJ, Jeffries KA, Paguio CG, Grodzinsky AJ. Cart""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,24,reference_content,"32. Franz T, Hasler EM, Hagg R, Weiler C, Jakob RP, Mainil-Varlet P. In situ compressive stiffness, biochemical composition, and structural integrity of articular cartilage of the human knee joint. Os","[634.0, 906.0, 1113.0, 1011.0]",reference_item,0.85,"[""reference content label: 32. Franz T, Hasler EM, Hagg R, Weiler C, Jakob RP, Mainil-V""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_dot,True,True +8,25,reference_content,"33. Stumpfe ST, Pester JK, Steinert S, Marintschev I, Plettenberg H, Aurich M, Hofmann GO. Is there a correlation between biophotonical, biochemical, histological, and visual changes in the cartilage ","[635.0, 1016.0, 1114.0, 1121.0]",reference_item,0.85,"[""reference content label: 33. 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"p15:27", + "p15:28", + "p15:29", + "p15:30" + ], + "findings": [ + { + "category": "same_page_boundary_error", + "severity": "major", + "block_ids": [], + "truth": "body/reference/backmatter boundaries should be explainable at block level", + "pipeline_behavior": "page contains mixed body/reference/tail signals", + "root_cause_hypothesis": "same-page boundary ambiguity", + "evidence": { + "annotated_page": "annotated_pages/page_013.png", + "artifact": "page_risk_summary.json" + } + }, + { + "category": "same_page_boundary_error", + "severity": "major", + "block_ids": [], + "truth": "body/reference/backmatter boundaries should be explainable at block level", + "pipeline_behavior": "page contains mixed body/reference/tail signals", + "root_cause_hypothesis": "same-page boundary ambiguity", + "evidence": { + "annotated_page": "annotated_pages/page_015.png", + "artifact": "page_risk_summary.json" + } + }, + { + "category": "render_mapping_error", + "severity": "minor", + "block_ids": [ + "p1:0", + "p1:2", + "p1:4", + "p1:8", + "p1:9", + "p1:11", + "p1:12", + "p1:13", + "p1:15", + "p1:17", + "p1:18", + "p1:19", + "p1:20", + "p1:21", + "p1:22", + "p1:23", + "p2:0", + "p2:12", + "p2:13", + "p2:14" + ], + "truth": "rendered fulltext should be traceable back to source blocks", + "pipeline_behavior": "some render-default blocks are not easily mapped into the current fulltext output", + "root_cause_hypothesis": "render omission or snippet mismatch", + "evidence": { + "annotated_page": null, + "artifact": "fulltext_block_mapping_summary.json" + } + } + ] +} \ No newline at end of file diff --git a/audit/82W2IJIP/audit_report.md b/audit/82W2IJIP/audit_report.md new file mode 100644 index 00000000..492f7f02 --- /dev/null +++ b/audit/82W2IJIP/audit_report.md @@ -0,0 +1,18 @@ +# OCR Truth Audit Report - 82W2IJIP + +- Mode: `high-risk` +- Status: `READY` +- Reviewed pages: [1, 3, 4, 6, 8, 10, 12, 13, 14, 15] +- Reviewed blocks: 211 + +## Findings + +- `major` `same_page_boundary_error`: page contains mixed body/reference/tail signals +- `major` `same_page_boundary_error`: page contains mixed body/reference/tail signals +- `minor` `render_mapping_error`: some render-default blocks are not easily mapped into the current fulltext output + +## Disposition Guidance + +- Use `repair` when the finding reflects a pipeline defect worth fixing now. +- Use `residual` when the finding is real but intentionally deferred. +- Do not rewrite expected truth to make current output look correct. diff --git a/audit/82W2IJIP/audit_scope.json b/audit/82W2IJIP/audit_scope.json new file mode 100644 index 00000000..e4749036 --- /dev/null +++ b/audit/82W2IJIP/audit_scope.json @@ -0,0 +1,1736 @@ +{ + "mode": "high-risk", + "selected_pages": [ + 1, + 3, + 4, + 6, + 8, + 10, + 12, + 13, + 14, + 15 + ], + "required_block_ids": [ + "p1:0", + "p1:1", + "p1:2", + "p1:3", + "p1:4", + "p1:5", + "p1:6", + "p1:7", + "p1:8", + "p1:9", + "p1:10", + "p1:11", + "p1:12", + "p1:13", 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label""]",noise,0.9,frontmatter_main_zone,support_like,none,False,False +1,3,doc_title,Mechano-Iontronic Hydrogels Generating Biomimetic Endogenous Bioelectricity for Promoting Cartilage Regeneration,"[96.0, 147.0, 992.0, 284.0]",paper_title,0.8,"[""page-1 zone title_zone: Mechano-Iontronic Hydrogels Generating Biomimetic Endogenous""]",paper_title,0.8,frontmatter_main_zone,support_like,none,True,True +1,4,text,"Longwei Li, Zheng Li,* Muxin Yue, Yangshi Shao, Jing Wang, Yutong Song, Zhong Lin Wang,* Yongsheng Zhou,* and Xiong Pu*","[96.0, 314.0, 923.0, 386.0]",authors,0.8,"[""page-1 zone author_zone: Longwei Li, Zheng Li,* Muxin Yue, Yangshi Shao, Jing Wang, Y""]",authors,0.8,frontmatter_main_zone,support_like,none,True,True +1,5,abstract,"Articular cartilage regeneration has long been a formidable challenge because of its avascular and aneural nature. Traditional approaches, using exogenous electrical stimulation or electroactive mater","[96.0, 447.0, 739.0, 893.0]",abstract_body,0.85,"[""abstract label from Paddle OCR""]",abstract_body,0.85,body_zone,body_like,none,True,True +1,6,paragraph_title,1. Introduction,"[97.0, 964.0, 246.0, 989.0]",section_heading,0.85,"[""paragraph_title label with numbering: 1. Introduction""]",section_heading,0.85,body_zone,heading_like,heading_numbered,True,True +1,7,text,"Articular cartilage injuries often result in chronic pain and impaired functionality, posing a significant challenge to patients' physical and mental well-being. $ ^{[1]} $ The limited repair capacity","[95.0, 1002.0, 588.0, 1094.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,8,text,"avascular and anneal nature, presenting substantial clinical challenges. $ ^{[2,3]} $ Consequently, it is of paramount importance to develop biomimetic scaffold materials with superior biocompatibilit","[763.0, 434.0, 1099.0, 960.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,9,text,relevant ion channels on the cell membrane (such as calcium ion channels). $ ^{[15-19]} $,"[605.0, 962.0, 1097.0, 1003.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,10,text,"In fact, bioelectricity is majorly in the form of iontronic electricity, that is, the electric field of unscreened ions or the electric current of ion flux. $ ^{[20,21]} $ For example, the bioelectric","[605.0, 1005.0, 1099.0, 1093.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +1,11,footnote,"L. 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China","[606.0, 1122.0, 902.0, 1198.0]",footnote,0.7,"[""footnote label: Y. Shao, J. Wang, Y. Song, Z. L. Wang, X. Pu \nSchool of Nan""]",footnote,0.7,body_zone,body_like,none,True,True +1,14,footnote,"Z. Li, Y. Zhou","[607.0, 1198.0, 705.0, 1219.0]",footnote,0.7,"[""footnote label: Z. Li, Y. 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China""]",footnote,0.7,body_zone,body_like,none,True,True +1,18,footnote,"M. Yue, Y. Zhou +Institute of Medical Technology +Peking University Health Science Center +Haidian District, Beijing 100191, P. R. China","[608.0, 1312.0, 909.0, 1386.0]",footnote,0.7,"[""footnote label: M. Yue, Y. Zhou\nInstitute of Medical Technology\nPeking Unive""]",footnote,0.7,body_zone,body_like,none,True,True +1,19,footer,DOI: 10.1002/adma.202514604,"[97.0, 1420.0, 341.0, 1443.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +1,20,footnote,"Z. L. Wang +Guangzhou Institute of Blue Energy +Knowledge City, Guangzhou 510555, P. R. China","[607.0, 1389.0, 935.0, 1444.0]",footnote,0.7,"[""footnote label: Z. L. Wang\nGuangzhou Institute of Blue Energy\nKnowledge City""]",footnote,0.7,body_zone,body_like,none,True,True +1,21,footer,"Adv. Mater. 2026, 38, e14604","[98.0, 1487.0, 270.0, 1505.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +1,22,number,e14604 (1 of 17),"[535.0, 1484.0, 659.0, 1508.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +1,23,footer,© 2025 Wiley-VCH GmbH,"[937.0, 1487.0, 1096.0, 1506.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +2,0,header,"ADVANCED +SCIENCE NEWS +www.advancedsciencenews.com","[92.0, 46.0, 339.0, 117.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +2,1,header_image,,"[936.0, 45.0, 1091.0, 116.0]",unknown_structural,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,body_zone,body_like,empty,False,True +2,2,text,"membrane is the foundation of life activities.[22] For cartilage, it has also been demonstrated that iontronic electric-potential could be generated under pressure deformation, resulting from the ion ","[89.0, 148.0, 582.0, 522.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,3,text,"Herein, we designed a mechano-iontronic hydrogel (MI-hydrogel) for promoting cartilage repair by mimicking the iontronic bioelectricity generation of natural cartilage. The MI-hydrogel, implanted in t","[89.0, 522.0, 582.0, 917.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,4,text,"Our MI-hydrogel presented obvious advantages for cartilage repair, including low infection risk, freedom from secondary surgery, superior convenience, and outstanding repair effect, compared with prev","[89.0, 916.0, 582.0, 1160.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,5,paragraph_title,2. Results and Discussion,"[91.0, 1185.0, 345.0, 1209.0]",section_heading,0.85,"[""paragraph_title label with numbering: 2. Results and Discussion""]",section_heading,0.85,body_zone,heading_like,heading_numbered,True,True +2,6,paragraph_title,2.1. Iontronic Electricity Generation in Cartilage and MI-Hydrogel,"[90.0, 1223.0, 581.0, 1247.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.1. Iontronic Electricity Generation in Cartilage and MI-Hy""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +2,7,text,"The iontronic electricity generation mechanisms of natural cartilage and our MI-hydrogel are compared schematically in Figure 2a. Generally, the cartilage or MI-hydrogel is a porous medium soaked with","[89.0, 1267.0, 582.0, 1444.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,8,text,,"[600.0, 149.0, 1093.0, 434.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +2,9,text,"To measure the iontronic electricity, cartilage or hydrogel samples were immersed in culture solution, and two gold electrodes were arranged at both ends of the bottom. An indenter was used to compres","[599.0, 433.0, 1093.0, 719.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,10,text,"For better understanding, finite-element simulations were conducted by combining Poroelastic mechanics and Poisson–Nernst–Planck equations to calculate the distribution of internal pore pressure, ion ","[599.0, 719.0, 1092.0, 1048.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,11,text,"For the MI-hydrogel, three samples were investigated, namely 7.5 wt.% PNAGA, 15 wt.% PNAGA + 0.9 wt.% NaCl, and 30 wt.% PNAGA + 0.9 wt.% NaCl. According to previous studies, the iontronic electricity ","[598.0, 1049.0, 1093.0, 1445.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +2,12,footer,"Adv. Mater. 2026, 38, e14604","[93.0, 1487.0, 264.0, 1505.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +2,13,number,e14604 (2 of 17),"[529.0, 1484.0, 654.0, 1508.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +2,14,footer,© 2025 Wiley-VCH GmbH,"[931.0, 1486.0, 1090.0, 1506.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +2,15,aside_text,"15214095, 2026, 2, Downloaded from https://advanced.onlinelibrary.wiley.com/doi/10.1002/adma.202514604 by Shandong University Library, Wiley Online Library on [05/04/2026]. See the Terms and Condition","[1155.0, 30.0, 1171.0, 1533.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +3,0,header,"ADVANCED +SCIENCE NEWS +www.advancedsciencenews.com","[98.0, 45.0, 345.0, 117.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +3,1,header_image,,"[942.0, 44.0, 1097.0, 116.0]",unknown_structural,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,body_zone,body_like,empty,False,True +3,2,image,,"[160.0, 144.0, 1036.0, 1123.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +3,3,figure_title,Figure 1. Mechano-iontronic effect for promoting cartilage regeneration. a) MI-hydrogel implanted in an articular cartilage defect. b) Mechano-iontronic conversion in MI-hydrogel. c) Comparison betwee,"[95.0, 1134.0, 1100.0, 1233.0]",figure_caption,0.92,"[""figure_title label: Figure 1. Mechano-iontronic effect for promoting cartilage r""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +3,4,text,"and 120 nA at 30% compression strain, significantly higher than 0.6 mV and 26.4 nA of 7.5 wt.% PNAGA hydrogel, respectively (summarized data in Figure 2f and profiles in Figure S5, Supporting Informat","[96.0, 1266.0, 588.0, 1445.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +3,5,text,,"[604.0, 1266.0, 1099.0, 1446.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +3,6,footer,"Adv. Mater. 2026, 38, e14604","[98.0, 1487.0, 270.0, 1505.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +3,7,number,e14604 (3 of 17),"[535.0, 1484.0, 659.0, 1508.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +3,8,footer,© 2025 Wiley-VCH GmbH,"[937.0, 1486.0, 1096.0, 1506.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +3,9,aside_text,"15214095, 2026, 2, Downloaded from https://advanced.onlinelibrary.wiley.com/doi/10.1002/adma.202514604 by Shandong University Library, Wiley Online Library on [05/04/2026]. See the Terms and Condition","[1155.0, 30.0, 1171.0, 1535.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +4,0,header,"ADVANCED +SCIENCE NEWS +www.advancedsciencenews.com","[92.0, 45.0, 340.0, 117.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +4,1,header,"ADVANCED MATERIALS +www.advmat.de","[936.0, 45.0, 1092.0, 116.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +4,2,figure_title,a,"[99.0, 151.0, 119.0, 171.0]",figure_inner_text,0.9,"[""panel label / figure inner text: a""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +4,3,figure_title,Mechano-iontronic conversion in cartilage,"[109.0, 180.0, 456.0, 201.0]",figure_caption,0.85,"[""figure_title label: Mechano-iontronic conversion in cartilage""]",figure_caption,0.85,body_zone,legend_like,none,True,True +4,4,image,,"[143.0, 208.0, 444.0, 347.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,5,image,,"[135.0, 357.0, 435.0, 415.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,6,image,,"[468.0, 185.0, 747.0, 347.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,7,image,,"[473.0, 356.0, 758.0, 412.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,8,figure_title,b,"[768.0, 150.0, 789.0, 175.0]",figure_inner_text,0.9,"[""panel label / figure inner text: b""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +4,9,image,,"[786.0, 156.0, 1087.0, 293.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,10,image,,"[800.0, 304.0, 1075.0, 405.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,11,figure_title,C,"[104.0, 463.0, 124.0, 483.0]",figure_inner_text,0.9,"[""panel label / figure inner text: C""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +4,12,chart,,"[112.0, 468.0, 418.0, 706.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,13,image,,"[466.0, 456.0, 693.0, 678.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,14,chart,,"[778.0, 448.0, 1084.0, 703.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,15,figure_title,f,"[106.0, 709.0, 122.0, 734.0]",figure_inner_text,0.9,"[""panel label / figure inner text: f""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +4,16,chart,,"[112.0, 712.0, 461.0, 994.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,17,image,,"[465.0, 711.0, 770.0, 923.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,18,chart,,"[778.0, 709.0, 1084.0, 960.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,19,chart,,"[118.0, 988.0, 426.0, 1231.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,20,chart,,"[491.0, 1000.0, 1052.0, 1232.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +4,21,figure_title,Figure 2. Mechano-iontronic conversion in cartilage and MI-hydrogel. a) Schematic illustration of the mechano-iontronic conversion in cartilage (left) and MI-hydrogel (right). b) Electrical signal tes,"[90.0, 1243.0, 1093.0, 1341.0]",figure_caption,0.92,"[""figure_title label: Figure 2. Mechano-iontronic conversion in cartilage and MI-h""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +4,22,footer,"Adv. Mater. 2026, 38, e14604","[93.0, 1487.0, 264.0, 1504.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +4,23,number,e14604 (4 of 17),"[529.0, 1485.0, 654.0, 1508.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +4,24,footer,© 2025 Wiley-VCH GmbH,"[931.0, 1487.0, 1090.0, 1506.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +4,25,aside_text,"15214095, 2026, 2, Downloaded from https://advanced.onlinelibrary.wiley.com/doi/10.1002/adma.202514604 by Shandong University Library, Wiley Online Library on [05/04/2026]. See the Terms and Condition","[1155.0, 30.0, 1171.0, 1534.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +5,0,header,"ADVANCED +SCIENCE NEWS +www.advancedsciencenews.com","[98.0, 46.0, 345.0, 117.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +5,1,header_image,,"[942.0, 45.0, 1097.0, 116.0]",unknown_structural,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,body_zone,body_like,empty,False,True +5,2,text,the MI-hydrogel was tested and its output remained stable for 5000 s ( $ \approx $1000 cycles) (Figure 2j). The rheological properties of the MI-hydrogel were also tested. Under room temperature condi,"[95.0, 149.0, 588.0, 303.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,3,text,"We also tested the degradation and swelling of the MI-hydrogel in the PBS (phosphate-buffered saline) solution in vitro, as well as the electrical properties under different periods (Figure S7, Suppor","[96.0, 303.0, 587.0, 501.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,4,paragraph_title,2.2. MI-Hydrogels Promote Chondrogenic Differentiation In Vitro,"[96.0, 543.0, 587.0, 566.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.2. MI-Hydrogels Promote Chondrogenic Differentiation In Vi""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +5,5,text,"We proposed that our MI-hydrogels, under physical stress, can generate endogenous bioelectricity-like electrical signals to promote chondrogenic differentiation of stem cells. In this context, bone ma","[96.0, 588.0, 588.0, 1268.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,6,text,Four control experiments were compared. The two hydrogels with the highest (30 wt.% PNAGA + 0.9 wt.% NaCl) and lowest (7.5 wt.% PNAGA) iontronic electrical outputs were defined as I+ and I− (iontronic,"[95.0, 1268.0, 588.0, 1445.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,7,text,,"[605.0, 149.0, 1098.0, 304.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +5,8,text,"At the gene and protein dimensions, SKY-box transcription factor 9 (SOX9), collagen type 11 alpha 1 chain (COL2A1), and aggrecan (ACAN) were selected as biomarkers to evaluate chondrogenic differentia","[605.0, 301.0, 1098.0, 1050.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,9,text,"Mechanically sensitive ion channels, namely Piezo proteins, are indispensable for mechano-transduction across diverse cellular contexts. Prior studies have emphasized the pivotal role of Piezo1 in med","[604.0, 1048.0, 1098.0, 1445.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +5,10,footer,"Adv. Mater. 2026, 38, e14604","[98.0, 1487.0, 270.0, 1505.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +5,11,number,e14604 (5 of 17),"[535.0, 1484.0, 659.0, 1508.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +5,12,footer,© 2025 Wiley-VCH GmbH,"[937.0, 1487.0, 1096.0, 1506.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +5,13,aside_text,"15214095, 2026, 2, Downloaded from https://advanced.onlinelibrary.wiley.com/doi/10.1002/adma.202514604 by Shandong University Library, Wiley Online Library on [05/04/2026]. See the Terms and Condition","[1155.0, 30.0, 1171.0, 1534.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +6,0,header,"ADVANCED +SCIENCE NEWS +www.advancedsciencenews.com","[92.0, 45.0, 339.0, 117.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +6,1,header_image,,"[937.0, 45.0, 1091.0, 116.0]",unknown_structural,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,body_zone,body_like,empty,False,True +6,2,figure_title,a,"[108.0, 156.0, 128.0, 178.0]",figure_inner_text,0.9,"[""panel label / figure inner text: a""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +6,3,image,,"[138.0, 154.0, 1058.0, 457.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,4,figure_title,b,"[108.0, 460.0, 130.0, 486.0]",figure_inner_text,0.9,"[""panel label / figure inner text: b""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +6,5,image,,"[136.0, 474.0, 1075.0, 936.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,6,figure_title,c,"[112.0, 956.0, 133.0, 979.0]",figure_inner_text,0.9,"[""panel label / figure inner text: c""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +6,7,chart,,"[157.0, 956.0, 428.0, 1230.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,8,figure_title,d,"[438.0, 951.0, 460.0, 977.0]",figure_inner_text,0.9,"[""panel label / figure inner text: d""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +6,9,chart,,"[463.0, 958.0, 745.0, 1227.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,10,figure_title,e,"[757.0, 955.0, 777.0, 977.0]",figure_inner_text,0.9,"[""panel label / figure inner text: e""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +6,11,chart,,"[784.0, 957.0, 1068.0, 1221.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +6,12,figure_title,Figure 3. Chondrogenic differentiation of BMSCs in MI-hydrogel under an applied pressure. a) Schematic representation of the mechanical stimulation on BMSCs in MI-hydrogel. The MI-hydrogel is compress,"[90.0, 1238.0, 1094.0, 1428.0]",figure_caption,0.92,"[""figure_title label: Figure 3. Chondrogenic differentiation of BMSCs in MI-hydrog""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +6,13,footer,"Adv. Mater. 2026, 38, e14604","[93.0, 1487.0, 264.0, 1504.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +6,14,number,e14604 (6 of 17),"[529.0, 1485.0, 654.0, 1507.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +6,15,footer,© 2025 Wiley-VCH GmbH,"[931.0, 1487.0, 1090.0, 1506.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +6,16,aside_text,"15214095, 2026, 2. Downloaded from https://advanced.onlinelibrary.wiley.com/doi/10.1002/adma.202514604 by Shandong University Library. Wiley Online Library on [05/04/2026]. See the Terms and Condition","[1154.0, 28.0, 1172.0, 1532.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +7,0,header,"ADVANCED +SCIENCE NEWS +www.advancedsciencenews.com","[98.0, 46.0, 345.0, 117.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +7,1,header_image,,"[942.0, 45.0, 1097.0, 116.0]",unknown_structural,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,body_zone,body_like,empty,False,True +7,2,text,"seventh and 14th day after chondrogenic induction. Clearly, the expression of Piezo1 in the iontronic hydrogel under the mechanical force group (I+ M+) was significantly higher than the other three gr","[95.0, 149.0, 587.0, 302.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,3,text,"To further validate the applicability of our findings, we conducted additional experiments using human adipose-derived mesenchymal stem cells (hADSCs). As shown in Figure S12 (Supporting Information),","[95.0, 303.0, 588.0, 525.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,4,paragraph_title,2.3. MI-Hydrogels Reinforce Cartilage Regeneration in Rats,"[95.0, 566.0, 541.0, 589.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.3. MI-Hydrogels Reinforce Cartilage Regeneration in Rats""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +7,5,text,"We performed in vivo investigations to assess the influence of our MI-hydrogel within rat knee joints, harnessing exercise-facilitated joint mobility as a means to expedite cartilage repair. For 4 and","[95.0, 609.0, 587.0, 1290.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,6,text,Histological examination of major organs was performed to assess systemic biocompatibility and long-term safety following implantation of the MI-hydrogel constructs. Hematoxylin and eosin (H&E) staini,"[95.0, 1290.0, 588.0, 1446.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,7,text,,"[605.0, 149.0, 1097.0, 215.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +7,8,text,"After 4 and 8 weeks of exercise, the knees were collected and analyzed using various methods, including macroscopic evaluation, new subchondral bone quantification, and histological evaluation. Overal","[606.0, 215.0, 1098.0, 655.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,9,text,"To further evaluate the regeneration of subchondral bone, we employed micro-computed tomography (micro-CT), demonstrating enhanced recovery of subchondral bone in iontronic hydrogel combined with the ","[605.0, 654.0, 1098.0, 1070.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,10,text,"Histological assessment including H&E staining, Safranin O/fast green staining (SOFG), and immunofluorescence staining of Col2a1 revealed the improved regeneration of hyaline cartilage within cartilag","[606.0, 1071.0, 1098.0, 1445.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +7,11,footer,"Adv. Mater. 2026, 38, e14604","[98.0, 1487.0, 270.0, 1505.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +7,12,number,e14604 (7 of 17),"[535.0, 1484.0, 659.0, 1508.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +7,13,footer,© 2025 Wiley-VCH GmbH,"[937.0, 1486.0, 1096.0, 1506.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +7,14,aside_text,"15214095, 2026, 2, Downloaded from https://advanced.onlinelibrary.wiley.com/doi/10.1002/adma.202514604 by Shandong University Library, Wiley Online Library on [05/04/2026]. See the Terms and Condition","[1154.0, 31.0, 1171.0, 1534.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +8,0,header,"ADVANCED +SCIENCE NEWS +www.advancedsciencenews.com","[91.0, 45.0, 339.0, 117.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +8,1,header,"ADVANCED MATERIALS +www.advmat.de","[936.0, 45.0, 1092.0, 116.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +8,2,image,,"[147.0, 157.0, 776.0, 478.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +8,3,chart,,"[819.0, 150.0, 1065.0, 333.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +8,4,chart,,"[818.0, 338.0, 1066.0, 507.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +8,5,figure_title,b,"[118.0, 503.0, 137.0, 526.0]",figure_inner_text,0.9,"[""panel label / figure inner text: b""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +8,6,image,,"[127.0, 505.0, 801.0, 833.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +8,7,chart,,"[811.0, 518.0, 1064.0, 681.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +8,8,chart,,"[819.0, 694.0, 1065.0, 874.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +8,9,image,,"[128.0, 875.0, 801.0, 1240.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +8,10,chart,,"[837.0, 885.0, 1064.0, 1056.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +8,11,chart,,"[814.0, 1077.0, 1063.0, 1231.0]",figure_asset,0.85,"[""media label: chart""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +8,12,figure_title,Figure 4. Promoted cartilage regeneration in vivo with MI-hydrogel implantation. a) Schematic representation and timeline of the experimentation on rats. Defects were created in the femoral knee joint,"[90.0, 1246.0, 1093.0, 1435.0]",figure_caption,0.92,"[""figure_title label: Figure 4. Promoted cartilage regeneration in vivo with MI-hy""]",figure_caption,0.92,display_zone,legend_like,figure_number,True,True +8,13,footer,"Adv. Mater. 2026, 38, e14604","[93.0, 1488.0, 264.0, 1504.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +8,14,number,e14604 (8 of 17),"[529.0, 1485.0, 654.0, 1507.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +8,15,footer,© 2025 Wiley-VCH GmbH,"[931.0, 1487.0, 1090.0, 1506.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +8,16,aside_text,"15214095, 2026, 2, Downloaded from https://advanced.onlinelibrary.wiley.com/doi/10.1002/adma.202514604 by Shandong University Library, Wiley Online Library on [05/04/2026]. See the Terms and Condition","[1155.0, 30.0, 1171.0, 1533.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +9,0,header,"ADVANCED +SCIENCE NEWS +www.advancedsciencenews.com","[98.0, 46.0, 345.0, 117.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +9,1,header_image,,"[942.0, 45.0, 1097.0, 116.0]",unknown_structural,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,body_zone,body_like,empty,False,True +9,2,text,"exercise, the iontronic hydrogel group demonstrated enhancement in cartilage regeneration (Figure 4b,f), potentially attributable to the spontaneous or passive movements of rats, which may have also p","[95.0, 149.0, 588.0, 564.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,3,text,"Gait analysis at 4 weeks revealed that rats in the I+M+ group exhibited markedly improved paw contact patterns, with larger and more uniform footprints compared to other defect groups (Figure S15a, Su","[95.0, 566.0, 588.0, 851.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,4,text,"Across in vivo outcomes, the omnibus one-way ANOVAs were overwhelmingly powered, with achieved power >0.95 for each outcome (noncentral F method; $ \lambda = \hat{f} \times N $, $ df_1 = 6 $, $ df_","[95.0, 851.0, 587.0, 1051.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,5,paragraph_title,2.4. Metabolic Rewiring Induced by MI-Hydrogel in Cartilage Repair,"[96.0, 1092.0, 553.0, 1137.0]",subsection_heading,0.85,"[""paragraph_title label with numbering: 2.4. Metabolic Rewiring Induced by MI-Hydrogel in Cartilage ""]",subsection_heading,0.85,body_zone,body_like,heading_numbered,True,True +9,6,text,"Piezo1 channels are activated in response to mechanical stimuli generated by movement, and their downstream signaling pathways are mainly regulated by activation of calcium channels within the cell me","[95.0, 1157.0, 587.0, 1376.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,7,text,"To unravel the metabolic events in the coupled mechano-iontronic effect contributing to cartilage repair, the articular cartilage was isolated from rats 4 and 8 weeks with or without exercise treatmen","[95.0, 1377.0, 588.0, 1444.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,8,text,,"[605.0, 150.0, 1098.0, 566.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,body_zone,body_like,empty,True,True +9,9,text,"Next, to detect the overlap of significantly differentially expressed metabolites in the four groups of I+ M+, I− M+, I+M−, and I− M−, the Venn diagram analysis on the fourth and eighth week was condu","[606.0, 566.0, 1098.0, 786.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,10,text,"A synergistic or exclusive interplay exists among diverse metabolites, and correlation analysis serves as a tool to quantify the metabolic proximities among notably distinct metabolites. This approach","[605.0, 785.0, 1098.0, 1444.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +9,11,footer,"Adv. Mater. 2026, 38, e14604","[98.0, 1487.0, 269.0, 1505.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +9,12,number,e14604 (9 of 17),"[535.0, 1484.0, 659.0, 1508.0]",noise,0.9,"[""page number label""]",noise,0.9,body_zone,body_like,short_fragment,False,False +9,13,footer,© 2025 Wiley-VCH GmbH,"[937.0, 1486.0, 1096.0, 1506.0]",noise,0.9,"[""footer label""]",noise,0.9,body_zone,body_like,none,False,False +9,14,aside_text,"15214095, 2026, 2, Downloaded from https://advanced.onlinelibrary.wiley.com/doi/10.1002/adma.202514604 by Shandong University Library, Wiley Online Library on [05/04/2026]. See the Terms and Condition","[1154.0, 31.0, 1171.0, 1532.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,body_zone,body_like,none,False,False +10,0,header,"ADVANCED +SCIENCE NEWS +www.advancedsciencenews.co","[90.0, 46.0, 323.0, 115.0]",noise,0.9,"[""header label""]",noise,0.9,body_zone,body_like,none,False,False +10,1,header_image,,"[936.0, 45.0, 1091.0, 116.0]",unknown_structural,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,body_zone,body_like,empty,False,True +10,2,figure_title,a,"[154.0, 153.0, 171.0, 171.0]",figure_inner_text,0.9,"[""panel label / figure inner text: a""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +10,3,image,,"[176.0, 160.0, 1010.0, 532.0]",figure_asset,0.85,"[""media label: image""]",media_asset,0.85,body_zone,unknown_like,empty,True,True +10,4,figure_title,b,"[158.0, 543.0, 177.0, 564.0]",figure_inner_text,0.9,"[""panel label / figure inner text: b""]",figure_inner_text,0.9,display_zone,legend_like,panel_label,True,True +10,5,table,"
MetabolitesClass II
Pos24681783
Neg17461418
Total42143201
GeneForward primer(5′-3′)Reverse primer(5′-3′)
GAPDHGGTCACCAGGGCTGCTTTTGGATCTCGCTCCTGGAAGATG
SOX9CCCTTCAAC,"[602.0, 187.0, 1087.0, 340.0]",table_html,0.85,"[""media label: table""]",media_asset,0.85,,unknown_like,none,True,True +14,9,text,"were blocked with 10% non-fat milk and incubated overnight at 4 °C with primary antibodies against COL2A1, p-CaMKII, CaMKII, GLS1, and $ \beta $-actin (internal control). After incubation with HRP-co","[600.0, 400.0, 1092.0, 552.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,,unknown_like,none,True,True +14,10,text,"Animal Experiments: Hydrogel precursor was placed into cylindrical molds with a diameter of 2 mm and a height of 1.5 mm, followed by UV light curing at a wavelength of 365 nm to prepare hydrogel sampl","[601.0, 552.0, 1092.0, 704.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,,unknown_like,none,True,True +14,11,text,"To establish a model of knee cartilage defects, SD rats were anesthetized via intraperitoneal injection of 1% pentobarbital and fixed in a supine position. The fur at the surgical site was shaved. Aft","[600.0, 705.0, 1092.0, 1444.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,,unknown_like,none,True,True +14,12,footer,"Adv. Mater. 2026, 38, e14604","[93.0, 1487.0, 264.0, 1504.0]",noise,0.9,"[""footer label""]",noise,0.9,,unknown_like,none,False,False +14,13,number,e14604 (14 of 17),"[525.0, 1484.0, 658.0, 1507.0]",noise,0.9,"[""page number label""]",noise,0.9,,unknown_like,short_fragment,False,False +14,14,footer,© 2025 Wiley-VCH GmbH,"[931.0, 1487.0, 1090.0, 1506.0]",noise,0.9,"[""footer label""]",noise,0.9,,unknown_like,none,False,False +14,15,aside_text,"15214095, 2026, 2, Downloaded from https://advanced.onlinelibrary.wiley.com/doi/10.1002/adma.202514604 by Shandong University Library, Wiley Online Library on [05/04/2026]. See the Terms and Condition","[1155.0, 30.0, 1171.0, 1534.0]",noise,0.95,"[""margin-band narrow/tall geometry; treated as noise""]",noise,0.95,,unknown_like,none,False,False +15,0,header,"ADVANCED +SCIENCE NEWS +www.advancedsciencenews.com","[98.0, 46.0, 345.0, 116.0]",noise,0.9,"[""header label""]",noise,0.9,,unknown_like,none,False,False +15,1,header_image,,"[942.0, 46.0, 1097.0, 116.0]",unknown_structural,0.2,"[""unrecognized label 'header_image'""]",unknown_structural,0.2,,unknown_like,empty,False,True +15,2,text,"S.O.-Fast Green Staining: Dehydrated paraffin sections by sequentially immersing them in xylene I for 20 min, xylene II for 20 min, absolute ethanol I for 5 min, absolute ethanol II for 5 min, and 75%","[96.0, 150.0, 587.0, 341.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,3,text,"Micro-CT Analysis and Histomorphometry Analysis: Utilizing an Inveon system (Siemens, Germany), Micro-CT imaging was conducted to assess new bone formation within the defect site. Subsequently, the co","[96.0, 342.0, 587.0, 605.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,4,text,"Gait Analysis: To evaluate the functional recovery of the operated limbs, gait analysis was performed. Rats from each group were allowed to walk freely across a transparent walkway equipped with an au","[97.0, 605.0, 587.0, 776.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,5,text,"Metabolic Analysis: The cartilage of rats in the iontronic hydrogel and exercise group (M+ 1+), non-iontronic hydrogel and exercise group (M+ 1-), iontronic hydrogel and no exercise group (M− 1+), and","[96.0, 776.0, 588.0, 1117.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,6,text,"Quantification of Glu, Gln, and $ \alpha $-KG Contents: The contents of glutamate (Glu), glutamine (Gln), and $ \alpha $-KG in the samples were measured using commercial assay kits (Elabscience, Chi","[96.0, 1117.0, 587.0, 1306.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,True,True +15,7,text,Enzyme Activity Assays: The activities of CS and $ \alpha $-KGDH were measured using commercial kits purchased from Sangon Biotech (China) following the manufacturers' protocols. GelMA-encapsulated c,"[96.0, 1306.0, 587.0, 1440.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,tail_nonref_hold_zone,unknown_like,none,True,True +15,8,text,,"[606.0, 151.0, 1097.0, 265.0]",ocr_text_missing,0.8,"[""ocr detected text region (raw_label=text) but no text extracted; no pdf backfill available""]",ocr_text_missing,0.8,,unknown_like,empty,True,True +15,9,text,"Statistical Analysis: Statistical analysis of the data was conducted using GraphPad Prism 8.2.1 software (GraphPad Software Inc., USA), with results presented as mean ± SD. For comparisons involving m","[606.0, 265.0, 1097.0, 437.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,10,paragraph_title,Supporting Information,"[607.0, 476.0, 839.0, 503.0]",backmatter_boundary_candidate,0.5,"[""backmatter boundary candidate: Supporting Information""]",backmatter_boundary_candidate,0.5,,heading_like,none,True,True +15,11,text,Supporting Information is available from the Wiley Online Library or from the author.,"[606.0, 514.0, 1096.0, 553.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,12,paragraph_title,Acknowledgements,"[608.0, 594.0, 800.0, 620.0]",sub_subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level sub_subsection_heading: Acknowledgements""]",sub_subsection_heading,0.6,body_zone,heading_like,short_fragment,True,True +15,13,text,"L.L., Z.L., and M.Y. contributed equally to this work. The authors acknowledge support from the grants of the National Natural Science Foundation of China (52173274, 82201023, 82270954), Hainan Provin","[606.0, 632.0, 1098.0, 786.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,14,paragraph_title,Conflict of Interest,"[608.0, 825.0, 792.0, 850.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Conflict of Interest""]",subsection_heading,0.6,body_zone,support_like,none,True,True +15,15,text,The authors declare no conflict of interest.,"[608.0, 862.0, 894.0, 884.0]",frontmatter_noise,0.88,"[""default body_paragraph for text label"", ""late role resolution: editorial phrase cross-validates non-body classification"", ""zone=body_zone"", ""style_family=support_like""]",body_paragraph,0.6,,support_like,none,False,False +15,16,paragraph_title,Data Availability Statement,"[608.0, 925.0, 872.0, 950.0]",subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level subsection_heading: Data Availability Statement""]",subsection_heading,0.6,body_zone,heading_like,none,True,True +15,17,text,The data that support the findings of this study are available from the corresponding author upon reasonable request.,"[606.0, 962.0, 1097.0, 1003.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,18,paragraph_title,Keywords,"[608.0, 1042.0, 707.0, 1068.0]",sub_subsection_heading,0.6,"[""unnumbered paragraph_title, inferred level sub_subsection_heading: Keywords""]",sub_subsection_heading,0.6,body_zone,heading_like,short_fragment,True,True +15,19,text,"cartilage repair, endogenous bioelectricity, mechano-iontronic effect, metabolic reprogramming","[606.0, 1080.0, 1096.0, 1121.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,20,text,"Received: July 29, 2025","[941.0, 1142.0, 1096.0, 1160.0]",body_paragraph,0.6,"[""default body_paragraph for text label""]",body_paragraph,0.6,body_zone,body_like,none,True,True +15,21,text,"Revised: September 7, 2025 +Published online: September 18, 2025","[841.0, 1157.0, 1096.0, 1195.0]",frontmatter_noise,0.88,"[""default body_paragraph for text label"", ""late role resolution: editorial phrase cross-validates non-body classification"", ""zone=body_zone"", ""style_family=support_like""]",body_paragraph,0.6,,support_like,none,False,False +15,22,reference_content,"[1] M. Wang, Y. Wu, G. Li, Q. Lin, W. Zhang, H. Liu, J. Su, Mater. Today Bio 2024, 24, 100948.","[617.0, 1264.0, 1096.0, 1302.0]",reference_item,0.85,"[""reference content label: [1] M. Wang, Y. Wu, G. Li, Q. Lin, W. Zhang, H. Liu, J. Su, ""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +15,23,reference_content,"[2] Z. Gu, J. Wang, Y. Fu, H. Pan, H. He, Q. Gan, C. Liu, Adv. Funct. Mater. 2023, 33, 2212561.","[619.0, 1304.0, 1095.0, 1341.0]",reference_item,0.85,"[""reference content label: [2] Z. Gu, J. Wang, Y. Fu, H. Pan, H. He, Q. Gan, C. Liu, Ad""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +15,24,reference_content,"[3] W. Hu, Y. Chen, C. Dou, S. Dong, Ann. Rheum. Dis. 2021, 80, 413.","[617.0, 1344.0, 1077.0, 1362.0]",reference_item,0.85,"[""reference content label: [3] W. Hu, Y. Chen, C. Dou, S. Dong, Ann. Rheum. Dis. 2021, ""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +15,25,reference_content,"[4] Y. Peng, Y. Zhuang, Y. Liu, H. Le, D. Li, M. Zhang, K. Liu, Y. Zhang, J. Zuo, J. Ding, Exploration 2023, 3, 20210043.","[619.0, 1364.0, 1095.0, 1400.0]",reference_item,0.85,"[""reference content label: [4] Y. Peng, Y. Zhuang, Y. Liu, H. Le, D. Li, M. Zhang, K. L""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +15,26,reference_content,"[5] C. Bertsch, H. Maréchal, V. Gribova, B. Lévy, C. Debry, P. Lavalle, L. Fath, Adv. Healthcare Mater. 2023, 12, 2203115.","[617.0, 1403.0, 1095.0, 1441.0]",reference_item,0.85,"[""reference content label: [5] C. Bertsch, H. Mar\u00e9chal, V. Gribova, B. L\u00e9vy, C. Debry, ""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +15,27,footer,"Adv. Mater. 2026, 38, e14604","[99.0, 1488.0, 270.0, 1505.0]",noise,0.9,"[""footer label""]",noise,0.9,,unknown_like,none,False,False +15,28,footer,e14604 (15 of 17),"[530.0, 1485.0, 664.0, 1507.0]",noise,0.9,"[""footer label""]",noise,0.9,,unknown_like,short_fragment,False,False +15,29,footer,© 2025 Wiley-VCH GmbH,"[937.0, 1487.0, 1096.0, 1506.0]",noise,0.9,"[""footer label""]",noise,0.9,,unknown_like,none,False,False +15,30,aside_text,"15214095, 2026, 2, Downloaded from https://advanced.onlinelibrary.wiley.com/doi/10.1002/adma.202514604 by Shandong University Library, Wiley Online Library on [05/04/2026]. 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Chen, Adv. Sci. 2024, 11, 2305363.","[610.0, 312.0, 1095.0, 347.0]",reference_item,0.85,"[""reference content label: [68] H. Li, Y. Yuan, L. Zhang, C. Xu, H. Xu, Z. Chen, Adv. S""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +17,9,reference_content,"[67] L. Yang, S. Venneti, D. Nagrath, Annu. Rev. Biomed. Eng. 2017, 19, 163.","[611.0, 271.0, 1095.0, 308.0]",reference_item,0.85,"[""reference content label: [67] L. Yang, S. Venneti, D. Nagrath, Annu. Rev. Biomed. Eng""]",reference_item,0.85,reference_zone,reference_like,reference_numeric_bracket,True,True +17,10,footer,"Adv. 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MetabolitesClass II
Pos
SamplesAbbreviationMNPs concentration ( $ \mu $L/mL)
Silk fibroinSF0
Silk fibroin scaffoldSFC0 2026-07-02 | 基于 500 篇 corpus 扫描 + 5 篇论文深挖 + +--- + +## P1: `(N)` 括号格式 ref 不识别 + +**根因**: 3 个检测点都不认 `(N)` 前缀 + +| 位置 | 文件 | 当前正则 | 缺失 | +|------|------|---------|------| +| `_REFERENCE_PATTERN` | `ocr_roles.py:72` | `\d+\.\s` / `et al.` | `\(\d+\)\s` | +| `_ref_number_sort_key` | `ocr_render.py:488` | `N.` / `N)` / `[N]` | `(N)` | +| `score_reference_entry.has_number_lead` | `ocr_reference_signals.py:37` | `[N]` / `N.` / `N)` / bare `N` | `(N)` | + +**影响**: 30/500 篇论文 (6%) 使用 `(N)` 格式，全部受影响 + +**9ZIJTI6J 实例**: 506 个 `(N)` 前缀 block，496 个被标为 `backmatter_body`（语意全错）。fulltext 渲染恰好正确因为 refs 在 post_reference_backmatter_zone 里被发射了——但排序用的是 backmatter 顺序而非 ref number 顺序。 + +**修复方案**: 三处统一加 `\((\d+)\)` 分支 + +--- + +## P2: Cross-page ref 角色不一致 + +**论文**: WNDJX4KB + +**现象**: +- 前 6 条 ref（page 8，与 heading 同页）→ `body_paragraph` +- 后 20 条 ref（page 9+）→ `reference_item` +- **所有 26 条 block 的 `raw_label` 都是 `reference_content`** + +**根因**: `assign_block_role` 阶段 raw_label=reference_content 正确分配 reference_item；但 `resolve_final_role` 对 page 8 的 block 没有做 zone-based 升级。这是因为 reference zone 在 heading 页（page 8）上还没完全建立（`reference_zone.status='HOLD'`），late resolution 时 zone-based 升级逻辑不生效。 + +**影响范围**: 跨页 ref 的 heading 页上第一条 ref 可能被 demote。发生在 heading 不在 pages[0] 位置的时候。 + +--- + +## P3: Ref 在 block 里但 fulltext 丢失 + +### 3a: KUR9PBJC — heading 被标成 subsection_heading + +"References and Notes" 被检测为 `subsection_heading`（`body_zone`）不是 `reference_heading`。导致 `reference_zone.status='HOLD'` → fulltext 结尾只有 publisher 水印，165 条 ref 没被组装成 reference section 渲染——实际上它们以 raw LaTeX 形式出现在 fulltext 但格式不完整，且 ref 147-149、159 在渲染过程中丢失。 + +**根因**: "References and Notes" 的 `paragraph_title` raw_label 进入了 heading resolution 但被分类为 subsection_heading 而非 reference_heading。 + +### 3b: U746UJ7G — 编号 40/41/43 渲染丢失 + +三条 ref（40/41/43）在 block 里是 `reference_item`、`render_default=True`、在 `reference_zone`，但 fulltext 没有。可能是排序或渲染阶段的截断问题（附近有 ref 41→42→44 跳过了 43）。 + +--- + +## P4: Reference heading 完全消失 — 4 篇 Wiley 论文 + +**97M7HFCD、2HEUD5P9、99JVAPSV、UV6IVNUE** + +### 现象 +- 4 篇全部**没有任何 block 包含 "References" 文本** +- 4 篇全部来自 Wiley 出版社（Advanced Science, Small Methods, Adv. Funct. Mater., Adv. Healthcare Mater.） +- 4 篇都有几百条 reference_item 在 reference_zone（部分编号格式异常："2409400"、"2301283"、"1909045" 等——这些是 Wiley 的 article tracking number 被误判为 ref） +- `reference_zone.status` 全部是 `'HOLD'`（heading_block_id=None） +- Fulltext **完全没有 Reference 章节** + +### 根因分析 +Wiley 这些 PDF 的 "References" heading 可能: +1. 被 OCR 识别为 noise/header（和杂志名跑头混在一起） +2. 以图形方式嵌在 PDF 里（非文本） +3. 被 `references_start` 定位正确（page=y=0.0）但具体 block 被分类为其他 role + +**核心问题**: 没有 reference_heading → pipeline 不渲染 ref section。即便有几百条 ref_items 也出不来。 + +### 次级问题: fake reference_item +这些论文里部分以数字开头的 text block 被 `_looks_like_reference` 误判为 reference_item（如 "2409400 (6 of 13)" 是 Wiley 的 article tracking footer，根本不是 ref）。需要在 `_looks_like_reference` 加长度/格式过滤。 + +--- + +## P5: Author bio 在 reference zone + +**论文**: 4AG67PBH + +### 现象 +- 3 条 author bio（"is a Ph.D. student...", "is assistant professor..."）在 `reference_zone` +- role 是 `backmatter_body`（role 对了但 zone 错了） +- `backmatter_start` 正确指向 page 25（bio 所在的 page） +- 但 zone inference 没有从 reference_zone 切换到 post_reference_backmatter_zone + +### 根因 +`reference_zone.status='HOLD'`（无 heading）→ zone inference 不知道 reference 在哪结束。backmatter content 被留在 reference_zone 里。这和后 4 个问题是同一个源头：**reference heading 缺失导致 zone boundary 不确定。** + +--- + +## 问题关联图 + +``` +reference heading 不被检测 + ├─→ P2: heading 同页的 ref 得不到 zone-based 升级 + ├─→ P3: reference_zone.status=HOLD → ref section 渲染不完整 + ├─→ P4: fulltext 完全没有 Reference 章节（最严重） + └─→ P5: zone boundary 不确定 → backmatter content 留在 ref zone + (4AG67PBH) + +(N) 格式不匹配 + └─→ P1: 6% 论文 ref 语义丢失 +``` + +--- + +## 修复优先级 + +| Priority | Problem | Why | Fix scope | +|----------|---------|-----|-----------| +| **P0** | P4: heading 完全消失 | 4 篇论文 fulltext 没有 ref 章节，最严重 | 需要查 Wiley PDF 的 "References" heading 为什么没被识别 | +| **P1** | P1: `(N)` 格式 | 6% 语料受影响，30 篇论文，修复简单 | 3 处 regex 统一加 `\((\d+)\)` | +| **P2** | P3: ref 渲染丢失 | 影响 fulltext 完整性 | 查渲染排序逻辑 | +| **P3** | P2: cross-page ref | 少量 block 受影响，低严重性 | resolve_final_role 需要处理 heading 页 | +| **P3** | P5: bios in ref zone | 边界 case，和 P3/P4 同根因 | heading 修好了这个跟着好 | diff --git a/audit/investigation-findings.md b/audit/investigation-findings.md new file mode 100644 index 00000000..e5699a1e --- /dev/null +++ b/audit/investigation-findings.md @@ -0,0 +1,77 @@ +# Investigation Findings — Evidence Complete + +> 2026-07-02 | Root causes confirmed for all 3 investigations + +--- + +## Investigation 3: WNDJX4KB — Root Cause Found + +### Evidence + +ALL 26 ref blocks (page 8 + page 9+) have identical fields: +- `raw_label=reference_content`, `seed_role=reference_item`, `style_family=reference_like`, `zone=reference_zone` +- **But page 8 blocks (1-6) final role = `body_paragraph`**, page 9+ (7-26) = `reference_item` +- Evidence only shows `["reference content label: ..."]` — NO evidence from `resolve_final_role` + +### Root Cause + +`assign_block_role()` correctly sets `reference_item` for ALL blocks. `resolve_final_role()` keeps it (no change). **The demotion happens AFTER `resolve_final_role`**, in `_normalize_reference_roles_from_partition()`. + +This function runs AFTER reference zone detection and partition. Blocks 1-6 on page 8 (same page as the "References" heading) are not included in the reference partition (the partition starts at a later page or y-position). The function demotes unpartitioned reference_item blocks to `body_paragraph` without recording evidence. + +### Fix + +Two options: +1. **Fix the partition** to include page 8 refs (all ref items below the heading) +2. **Fix `_normalize_reference_roles_from_partition`** to not demote blocks with `raw_label=reference_content` or `seed_role=reference_item` in `reference_zone` + +Option 1 is more correct — the partition should include ALL ref items below the heading on the heading page. + +--- + +## Investigation 4: Wiley Heading — Root Cause Found + +### Evidence + +Both `97M7HFCD` (page 6) and `2HEUD5P9` (page 18): +- `references_start` page has body subsections, publisher watermarks, running headers — **NO "References" heading text** +- No block in the entire paper contains "References", "REFERENCES", or any variant +- `reference_zone.status=HOLD`, `heading_block_id=None` +- Pipeline set `references_start` based on first `reference_item` block page, not on heading detection +- The "References" heading is **not present in the OCR text layer at all** + +### Root Cause + +The "References" heading in these Wiley PDFs is not extracted as text by PaddleOCR. Possible reasons: +1. Running header format: `ADVANCED SCIENCE NEWS\nwww.advancedsciencenews.com` occupies the header zone and may overlap with or replace the section heading slot +2. The heading is embedded in a graphical element (PDF vector text that PaddleOCR skips) +3. The heading uses a font variant that PaddleOCR classifies as noise/header_image + +**This is an OCR pipeline limitation — no code fix exists.** The text simply isn't available in the block layer. Synthetic heading would be risky (page 6 of 97M7HFCD is still body text, not a reference section; the `reference_item` blocks on page 6 are fake article tracking numbers like "2409400"). + +--- + +## Investigation 5: U746UJ7G — Root Cause Found + +### Evidence + +Refs 40, 41, 43 in blocks: +- All 3 ARE in `structured_blocks.jsonl`: `role=reference_item`, `zone=reference_zone`, `render_default=True`, page 12 +- None in fulltext (total 43 refs in fulltext vs 46 in blocks) +- Fulltext ref 42 = "Baghdadi JD, **Brook RH**..." (block ref 43 content!) +- Block ref 42 = "**Rhee C**, Wang R..." (different author, different paper) +- Total ref_items in blocks: 46 across pages 10, 11, 12 + +### Root Cause + +This is a **reference numbering collision**. The fulltext has ref 42 mapped to what the block system calls ref 43. Refs 40, 41 got dropped in the collision. + +Two possible mechanisms: +1. **Duplicate ref numbers**: If two blocks claim `42`, the rendering's dedup drops the original 42 (Rhee C) and the duplicates 40/41 (which share a prefix collision with 42's first block) +2. **Block ID collision** in consumed_table_block_keys or similar dedup structure (same P0 pattern — flat dict overwrites same-key entries) + +Likely: `_ref_number_sort_key` groups refs by number, and multiple blocks with the same number cause a dedup collision. The fulltext has the LAST instance of number 42, not the first. + +### Fix + +Add a `_ref_number_dedup` guard in `_reorder_tail_run()` or the render emit path that logs/detects duplicate ref numbers. If a block's ref number is already emitted, append a disambiguation suffix rather than silently dropping. diff --git a/audit/reference-zone-audit.json b/audit/reference-zone-audit.json new file mode 100644 index 00000000..616b940f --- /dev/null +++ b/audit/reference-zone-audit.json @@ -0,0 +1,991 @@ +[ + { + "key": "9QKBD38Z", + "errors": [], + "warnings": [], + "reference": { + "status": "no_ref_section", + "count": 0, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "DLVSVU49", + "errors": [], + "warnings": [], + "reference": { + "status": "no_ref_section", + "count": 0, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "37LK5T97", + "errors": [], + "warnings": [ + "ref_ordering: 1 issues" + ], + "reference": { + "status": "issues", + "count": 116, + "numbered_count": 116, + "expected_last": 116, + "issues": [ + { + "type": "missing_numbers", + "count": 2, + "missing": [ + 100, + 101 + ] + } + ] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "B43QSAJP", + "errors": [], + "warnings": [ + "ref_ordering: 1 issues" + ], + "reference": { + "status": "issues", + "count": 52, + "numbered_count": 52, + "expected_last": 52, + "issues": [ + { + "type": "missing_numbers", + "count": 2, + "missing": [ + 17, + 18 + ] + } + ] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "A35UYJBK", + "errors": [], + "warnings": [], + "reference": { + "status": "no_ref_section", + "count": 0, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "95FDVE4W", + "errors": [], + "warnings": [ + "ref_ordering: 1 issues" + ], + "reference": { + "status": "issues", + "count": 23, + "numbered_count": 23, + "expected_last": 23, + "issues": [ + { + "type": "missing_numbers", + "count": 1, + "missing": [ + 2 + ] + } + ] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "82W2IJIP", + "errors": [], + "warnings": [], + "reference": { + "status": "no_ref_section", + "count": 0, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "72D4YXEB", + "errors": [], + "warnings": [], + "reference": { + "status": "ok", + "count": 33, + "numbered_count": 33, + "expected_last": 33, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "62LTMCI8", + "errors": [], + "warnings": [ + "ref_ordering: 1 issues" + ], + "reference": { + "status": "issues", + "count": 147, + "numbered_count": 147, + "expected_last": 147, + "issues": [ + { + "type": "missing_numbers", + "count": 5, + "missing": [ + 139, + 140, + 141, + 142, + 143 + ] + } + ] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "53B47JM8", + "errors": [], + "warnings": [ + "ref_ordering: 2 issues" + ], + "reference": { + "status": "issues", + "count": 65, + "numbered_count": 65, + "expected_last": 65, + "issues": [ + { + "type": "duplicate_number", + "number": 36, + "text": "[36] K.C. 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"missing_numbers", + "count": 17, + "missing": [ + 19, + 20, + 21, + 22, + 23, + 24, + 25, + 26, + 46, + 47, + 48, + 49, + 50, + 51, + 52, + 188, + 226 + ] + } + ] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "PMFECT33", + "errors": [], + "warnings": [], + "reference": { + "status": "no_ref_section", + "count": 0, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "M23R849F", + "errors": [], + "warnings": [], + "reference": { + "status": "no_ref_section", + "count": 0, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "JQMRCEXY", + "errors": [], + "warnings": [ + "ref_ordering: 1 issues" + ], + "reference": { + "status": "issues", + "count": 16, + "numbered_count": 16, + "expected_last": 16, + "issues": [ + { + "type": "missing_numbers", + "count": 5, + "missing": [ + 16, + 17, + 18, + 19, + 20 + ] + } + ] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "IPVHC44X", + "errors": [], + "warnings": [], + "reference": { + "status": "no_ref_section", + "count": 0, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "EUXKIYZM", + "errors": [], + "warnings": [], + "reference": { + "status": "no_ref_section", + "count": 0, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "BKKR4KIV", + "errors": [], + "warnings": [], + "reference": { + "status": "ok", + "count": 53, + "numbered_count": 53, + "expected_last": 53, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "99JVAPSV", + "errors": [], + "warnings": [], + "reference": { + "status": "no_ref_section", + "count": 0, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "2BB8VM5W", + "errors": [], + "warnings": [], + "reference": { + "status": "ok", + "count": 53, + "numbered_count": 53, + "expected_last": 53, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + }, + { + "key": "W33NLVJ2", + "errors": [], + "warnings": [], + "reference": { + "status": "no_ref_section", + "count": 0, + "issues": [] + }, + "block_stats": {}, + "reference_zone": { + "status": "no_structure" + }, + "inventory": {} + } +] \ No newline at end of file diff --git a/audit/zone-role-batch-audit-report.md b/audit/zone-role-batch-audit-report.md new file mode 100644 index 00000000..b057df00 --- /dev/null +++ b/audit/zone-role-batch-audit-report.md @@ -0,0 +1,293 @@ +# OCR Zone/Role Batch Audit Report + +Scanned 200 papers + +Total suspicious papers (score >= 1): 185 + +## Unknown Structural Blocks + +Total papers with unknown_structural: 181/200 +Total unknown blocks: 2729 + +By zone: +- body: 1784 +- frontmatter: 193 +- reference: 18 +- backmatter: 5 + +Worst papers: +- **WS6T79MU**: total=104 (fm=0 body=48 bm=0 ref=0) Author Manuscript +- **JLFF4L85**: total=94 (fm=2 body=92 bm=0 ref=0) +- **Y9LM7XNH**: total=68 (fm=0 body=25 bm=0 ref=0) The influence of radiographic viewing perspective and demographics on the Critic +- **4IG7M4FI**: total=56 (fm=1 body=43 bm=0 ref=0) Emerging Trends of Nanofibrous Piezoelectric and Triboelectric Applications: Mec +- **XVGX9U4V**: total=56 (fm=0 body=33 bm=0 ref=1) Nanoreinforced Hydrogels for Tissue Engineering: Biomaterials that are Compatibl +- **XEK3VB67**: total=56 (fm=2 body=40 bm=0 ref=0) Unleashing the Potential of Electroactive Hybrid Biomaterials and Self-Powered S +- **TLR5T8W4**: total=48 (fm=0 body=12 bm=0 ref=0) Migration Responses of Outer and Inner Meniscus Cells to Applied Direct Current +- **U26YPHMW**: total=47 (fm=1 body=18 bm=0 ref=0) World Journal of +Clinical Cases +- **ZAJWC3SA**: total=45 (fm=0 body=24 bm=0 ref=0) Characterization of Chondrocyte Scaffold Carriers for Cell-based Gene Therapy in +- **WDCPZHE5**: total=44 (fm=0 body=37 bm=0 ref=0) A Review of Vagus Nerve Stimulation for Disease: Comprehensive Theory and Eviden +- **WJNEHSQD**: total=40 (fm=0 body=40 bm=0 ref=0) Numerical Simulation of Electroactive Hydrogels for Cartilage-Tissue Engineering +- **TS623M5V**: total=37 (fm=0 body=26 bm=0 ref=0) Implantable Self-Powered Systems for Electrical Stimulation Medical Devices +- **XGT9Z257**: total=32 (fm=2 body=28 bm=0 ref=1) AI-based diagnosis of acute aortic syndrome from noncontrast CT +- **WXLHDCDM**: total=32 (fm=1 body=31 bm=0 ref=0) Evidence of Interlinks between Bioelectromagnetics and Biomechanics: from Biophy +- **XIR7ZJ6F**: total=30 (fm=1 body=18 bm=0 ref=0) Tissue Engineering Strategies to Increase Osteochondral Regeneration of Stem Cel +## Backmatter Patterns + +### body_paragraph in backmatter zone: 1 papers +- **9ZIJTI6J**: 6 blocks — Advances in Bioresorbable Triboelectric Nanogenerators + +### Author Contributions: 70 papers +- **PMFECT33**: 2 blocks, roles={'footnote': 1, 'body_paragraph': 1}, zones={'body_zone': 2} +- **TXMVULD7**: 1 blocks, roles={'body_paragraph': 1}, zones={'body_zone': 1} +- **58UFL9UN**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **62LTMCI8**: 1 blocks, roles={'body_paragraph': 1}, zones={'body_zone': 1} +- **B43QSAJP**: 1 blocks, roles={'unknown_structural': 1}, zones={'tail_nonref_hold_zone': 1} +- **JLFF4L85**: 1 blocks, roles={'section_heading': 1}, zones={'body_zone': 1} +- **LIGD5965**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **53B47JM8**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **49NUE2G7**: 1 blocks, roles={'unknown_structural': 1}, zones={'tail_nonref_hold_zone': 1} +- **U746UJ7G**: 1 blocks, roles={'body_paragraph': 1}, zones={'body_zone': 1} + +### Conflict of Interest: 112 papers +- **VFS8CBW2**: 2 blocks, roles={'body_paragraph': 2}, zones={'body_zone': 1, 'tail_nonref_hold_zone': 1} +- **3CEUN7T3**: 1 blocks, roles={'frontmatter_noise': 1}, zones={'body_zone': 1} +- **97M7HFCD**: 1 blocks, roles={'unknown_structural': 1}, zones={'tail_nonref_hold_zone': 1} +- **ES23M9IS**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **BKKR4KIV**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **WV2FF4NV**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **TXMVULD7**: 1 blocks, roles={'frontmatter_noise': 1}, zones={'body_zone': 1} +- **JQMRCEXY**: 1 blocks, roles={'body_paragraph': 1}, zones={'body_zone': 1} +- **58UFL9UN**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **62LTMCI8**: 1 blocks, roles={'frontmatter_noise': 1}, zones={'body_zone': 1} + +### Data Availability: 49 papers +- **XGT9Z257**: 2 blocks, roles={'subsection_heading': 2}, zones={'body_zone': 2} +- **WVB9LEFM**: 2 blocks, roles={'subsection_heading': 2}, zones={'body_zone': 2} +- **UBM39DTB**: 2 blocks, roles={'subsection_heading': 2}, zones={'body_zone': 2} +- **97M7HFCD**: 1 blocks, roles={'unknown_structural': 1}, zones={'tail_nonref_hold_zone': 1} +- **ES23M9IS**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **BKKR4KIV**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **WV2FF4NV**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **TXMVULD7**: 1 blocks, roles={'body_paragraph': 1}, zones={'body_zone': 1} +- **58UFL9UN**: 1 blocks, roles={'body_paragraph': 1}, zones={'body_zone': 1} +- **62LTMCI8**: 1 blocks, roles={'body_paragraph': 1}, zones={'body_zone': 1} + +### Ethics Statements: 20 papers +- **95FDVE4W**: 3 blocks, roles={'footnote': 1, 'subsection_heading': 1, 'body_paragraph': 1}, zones={'body_zone': 3} +- **ZFNT2XS7**: 3 blocks, roles={'body_paragraph': 2, 'subsection_heading': 1}, zones={'body_zone': 3} +- **3CEUN7T3**: 2 blocks, roles={'body_paragraph': 2}, zones={'body_zone': 2} +- **TXMVULD7**: 1 blocks, roles={'body_paragraph': 1}, zones={'body_zone': 1} +- **72D4YXEB**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **NSV8KBJY**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **MYWRV652**: 1 blocks, roles={'unknown_structural': 1}, zones={'tail_nonref_hold_zone': 1} +- **7CIULR7G**: 1 blocks, roles={'subsection_heading': 1}, zones={'body_zone': 1} +- **ZLSXVG2Y**: 1 blocks, roles={'body_paragraph': 1}, zones={'body_zone': 1} +- **YSKXZHDZ**: 1 blocks, roles={'footnote': 1}, zones={'body_zone': 1} + +### Author Bios: 1 papers +- **9ZIJTI6J**: 1 blocks, roles={'media_asset': 1}, zones={'body_zone': 1} + +### Supplementary Material: 46 papers +- **97M7HFCD**: 2 blocks, roles={'backmatter_boundary_candidate': 1, 'body_paragraph': 1}, zones={'unzoned': 1, 'tail_nonref_hold_zone': 1} +- **B43QSAJP**: 2 blocks, roles={'backmatter_boundary_candidate': 1, 'body_paragraph': 1}, zones={'body_zone': 1, 'unzoned': 1} +- **4CML4K3Y**: 2 blocks, roles={'body_paragraph': 2}, zones={'body_zone': 2} +- **LIGD5965**: 2 blocks, roles={'subsection_heading': 1, 'body_paragraph': 1}, zones={'body_zone': 2} +- **82W2IJIP**: 2 blocks, roles={'backmatter_boundary_candidate': 1, 'body_paragraph': 1}, zones={'unzoned': 1, 'body_zone': 1} +- **53B47JM8**: 2 blocks, roles={'reference_item': 1, 'body_paragraph': 1}, zones={'reference_zone': 1, 'body_zone': 1} +- **49NUE2G7**: 2 blocks, roles={'reference_item': 1, 'body_paragraph': 1}, zones={'reference_zone': 1, 'body_zone': 1} +- **H84PP2IW**: 2 blocks, roles={'backmatter_boundary_candidate': 1, 'body_paragraph': 1}, zones={'unzoned': 1, 'tail_nonref_hold_zone': 1} +- **W33NLVJ2**: 2 blocks, roles={'body_paragraph': 1, 'backmatter_boundary_candidate': 1}, zones={'frontmatter_main_zone': 1, 'body_zone': 1} +- **4AG67PBH**: 2 blocks, roles={'backmatter_boundary_candidate': 1, 'body_paragraph': 1}, zones={'unzoned': 1, 'body_zone': 1} + +### Disclaimer (Open Access misclassified): 5 papers +- **95FDVE4W**: 1 blocks, roles={'body_paragraph': 1}, zones={'body_zone': 1} +- **U746UJ7G**: 1 blocks, roles={'footnote': 1}, zones={'body_zone': 1} +- **WML2NNFE**: 1 blocks, roles={'footnote': 1}, zones={'': 1} +- **WEFRCCCH**: 1 blocks, roles={'body_paragraph': 1}, zones={'body_zone': 1} +- **TZ5XX44L**: 1 blocks, roles={'body_paragraph': 1}, zones={'tail_nonref_hold_zone': 1} + +## Reference Zone Patterns + +### Backmatter/body leaking into reference zone: 5 papers +- **9ZIJTI6J**: 600 blocks — Advances in Bioresorbable Triboelectric Nanogenerators +- **DWQQK2YB**: 12 blocks — Magnetoresponsive Stem Cell Spheroid-based Cartilage Recovery +Platform Utilizing +- **WNDJX4KB**: 6 blocks — Preliminary clinical outcomes of the double-row anchor suture-bridge technique f +- **4AG67PBH**: 3 blocks — Gathering Evidence to Leverage Musculoskeletal Magnetic Stimulation Towards Clin +- **VFS8CBW2**: 1 blocks — Directionalities of magnetic fields and topographic scaffolds synergise to enhan + +### Reference number gaps: 57 papers +- **99JVAPSV**: gaps at ref# 1, 2, 3, 4, 5, 6, 7, 8 — Piezoelectric Nano-Biomaterials for Biomedicine and Tissue Regeneration +- **VFS8CBW2**: gaps at ref# 1, 2, 3, 4, 5, 6, 7, 8 — Directionalities of magnetic fields and topographic scaffolds synergise to enhan +- **ZLSXVG2Y**: gaps at ref# 149, 150, 151, 152, 153, 154, 155, 156 — Advantages and Prospective Implications of Smart Materials in Tissue Engineering +- **TZ5XX44L**: gaps at ref# 4, 5, 6, 7, 8, 9, 11, 12 — Comparison of Machine Learning Methods With National Cardiovascular Data Registr +- **U8KUR7W5**: gaps at ref# 68, 116, 117, 122, 123, 124, 125 — Electrical stimulation as a novel tool for regulating cell behavior in tissue en +- **UVV6WCCV**: gaps at ref# 14, 47, 62, 63, 64, 65 — Voltage-Dependent Calcium Channels in Chondrocytes: Roles in Health and Disease +- **ES23M9IS**: gaps at ref# 1, 2, 3, 4, 5 — Magnetic Hydrogel for Cartilage Tissue Regeneration as well as a Review on Advan +- **Z73N29KR**: gaps at ref# 21, 23, 24, 29, 30 — Assessment of bone quality in the proximal humerus by measurement of the contral +- **WXLHDCDM**: gaps at ref# 1, 2, 3, 4, 5 — Evidence of Interlinks between Bioelectromagnetics and Biomechanics: from Biophy +- **VL5KKBZM**: gaps at ref# 33, 34, 35, 37, 38 — Acquired Acromion Compromise, Including Thinning and Fragmentation, Is Not Assoc + +## Degraded Mode Papers + +1 papers in degraded mode (layout fallback): +- **V4UTP5X7**: score=2 — Callus Formation by Electret + +## Zone-Role Anomalies + +### body_zone +Unexpected roles (appearing in ≥2 papers): +- **body_paragraph**: 196 papers +- **noise**: 195 papers +- **section_heading**: 189 papers +- **subsection_heading**: 178 papers +- **figure_asset**: 170 papers +- **unknown_structural**: 164 papers +- **footnote**: 151 papers +- **frontmatter_noise**: 137 papers +- **sub_subsection_heading**: 135 papers +- **media_asset**: 107 papers +- **table_html**: 99 papers +- **figure_caption_candidate**: 76 papers +- **abstract_body**: 59 papers +- **figure_caption**: 54 papers +- **ocr_text_missing**: 51 papers +- **affiliation**: 49 papers +- **non_body_insert**: 45 papers +- **structured_insert**: 25 papers +- **backmatter_boundary_candidate**: 19 papers +- **frontmatter_support**: 18 papers +- **abstract_heading**: 14 papers +- **structured_insert_candidate**: 13 papers +- **authors**: 13 papers +- **backmatter_heading**: 11 papers +- **figure_inner_text**: 10 papers +- **reference_item**: 10 papers +- **backmatter_body**: 10 papers +- **author_bio_asset**: 3 papers +- **paper_title**: 3 papers + +### display_zone +Unexpected roles (appearing in ≥2 papers): +- **figure_caption**: 182 papers +- **table_caption**: 111 papers +- **figure_inner_text**: 107 papers +- **body_paragraph**: 27 papers +- **non_body_insert**: 3 papers + +### frontmatter_main_zone +Unexpected roles (appearing in ≥2 papers): +- **non_body_insert**: 76 papers +- **structured_insert**: 29 papers +- **ocr_text_missing**: 22 papers +- **footnote**: 15 papers +- **figure_inner_text**: 6 papers + +### frontmatter_side_zone +Unexpected roles (appearing in ≥2 papers): +- **frontmatter_noise**: 26 papers +- **unknown_structural**: 15 papers +- **structured_insert**: 3 papers +- **body_paragraph**: 2 papers + +### post_reference_backmatter_zone +Unexpected roles (appearing in ≥2 papers): +- **unknown_structural**: 3 papers +- **backmatter_body**: 3 papers +- **sub_subsection_heading**: 2 papers + +### preproof_cover_zone +Unexpected roles (appearing in ≥2 papers): +- **frontmatter_noise**: 2 papers + +### reference_zone +Unexpected roles (appearing in ≥2 papers): +- **reference_item**: 196 papers +- **reference_heading**: 165 papers +- **noise**: 27 papers +- **unknown_structural**: 11 papers +- **footnote**: 3 papers + +### tail_nonref_hold_zone +Unexpected roles (appearing in ≥2 papers): +- **body_paragraph**: 112 papers +- **noise**: 75 papers +- **unknown_structural**: 67 papers +- **sub_subsection_heading**: 36 papers +- **figure_asset**: 30 papers +- **section_heading**: 27 papers +- **figure_caption_candidate**: 27 papers +- **backmatter_body**: 25 papers +- **figure_inner_text**: 19 papers +- **figure_caption**: 17 papers +- **table_caption**: 11 papers +- **table_html**: 10 papers +- **subsection_heading**: 9 papers +- **structured_insert**: 9 papers +- **footnote**: 7 papers +- **media_asset**: 7 papers +- **structured_insert_candidate**: 2 papers +- **backmatter_heading**: 2 papers + +### unzoned +Unexpected roles (appearing in ≥2 papers): +- **noise**: 182 papers +- **unknown_structural**: 82 papers +- **body_paragraph**: 58 papers +- **figure_asset**: 54 papers +- **reference_item**: 40 papers +- **footnote**: 33 papers +- **ocr_text_missing**: 32 papers +- **media_asset**: 31 papers +- **figure_caption_candidate**: 29 papers +- **backmatter_boundary_candidate**: 19 papers +- **figure_caption**: 19 papers +- **table_html**: 18 papers +- **frontmatter_noise**: 17 papers +- **sub_subsection_heading**: 12 papers +- **backmatter_body**: 10 papers +- **backmatter_heading**: 10 papers +- **subsection_heading**: 10 papers +- **section_heading**: 9 papers +- **author_bio_asset**: 6 papers +- **structured_insert**: 6 papers +- **abstract_body**: 2 papers +- **non_body_insert**: 2 papers + +## Top 30 Most Suspicious Papers + +- **9ZIJTI6J** score=615 unknown=8 patterns=frontmatter_unknown=1|body_unknown=4|backmatter_unknown=3|body_in_backmatter=6 | Advances in Bioresorbable Triboelectric Nanogenerators +- **WS6T79MU** score=104 unknown=104 patterns=body_unknown=48|render_blocked=217 | Author Manuscript +- **JLFF4L85** score=94 unknown=94 patterns=frontmatter_unknown=2|body_unknown=92|contrib=1|conflict=1 | +- **Y9LM7XNH** score=68 unknown=68 patterns=body_unknown=25|ethics=1|render_blocked=147 | The influence of radiographic viewing perspective and demographics on the Critic +- **XEK3VB67** score=58 unknown=56 patterns=frontmatter_unknown=2|body_unknown=40|contrib=1|conflict=1 | Unleashing the Potential of Electroactive Hybrid Biomaterials and Self-Powered S +- **4IG7M4FI** score=56 unknown=56 patterns=frontmatter_unknown=1|body_unknown=43|conflict=1|render_blocked=251 | Emerging Trends of Nanofibrous Piezoelectric and Triboelectric Applications: Mec +- **XVGX9U4V** score=56 unknown=56 patterns=body_unknown=33|ref_unknown=1|render_blocked=202 | Nanoreinforced Hydrogels for Tissue Engineering: Biomaterials that are Compatibl +- **TLR5T8W4** score=48 unknown=48 patterns=body_unknown=12|render_blocked=111 | Migration Responses of Outer and Inner Meniscus Cells to Applied Direct Current +- **U26YPHMW** score=47 unknown=47 patterns=frontmatter_unknown=1|body_unknown=18|contrib=1|ethics=1 | World Journal of +Clinical Cases +- **ZAJWC3SA** score=45 unknown=45 patterns=body_unknown=24|conflict=1|render_blocked=100 | Characterization of Chondrocyte Scaffold Carriers for Cell-based Gene Therapy in +- **WDCPZHE5** score=44 unknown=44 patterns=body_unknown=37|conflict=1|data_avail=1|render_blocked=299 | A Review of Vagus Nerve Stimulation for Disease: Comprehensive Theory and Eviden +- **WJNEHSQD** score=42 unknown=40 patterns=body_unknown=40|contrib=1|conflict=1|ref_gaps=100,101 | Numerical Simulation of Electroactive Hydrogels for Cartilage-Tissue Engineering +- **TS623M5V** score=37 unknown=37 patterns=body_unknown=26|conflict=1|render_blocked=223 | Implantable Self-Powered Systems for Electrical Stimulation Medical Devices +- **WXLHDCDM** score=37 unknown=32 patterns=frontmatter_unknown=1|body_unknown=31|ref_gaps=1,2,3,4,5|render_blocked=91 | Evidence of Interlinks between Bioelectromagnetics and Biomechanics: from Biophy +- **XGT9Z257** score=32 unknown=32 patterns=frontmatter_unknown=2|body_unknown=28|ref_unknown=1|contrib=1 | AI-based diagnosis of acute aortic syndrome from noncontrast CT +- **XD2BPCMG** score=30 unknown=29 patterns=frontmatter_unknown=1|body_unknown=23|contrib=1|conflict=1 | Overcoming challenges in cartilage regeneration: The role of chondrogenic induce +- **XIR7ZJ6F** score=30 unknown=30 patterns=frontmatter_unknown=1|body_unknown=18|contrib=1|conflict=1 | Tissue Engineering Strategies to Increase Osteochondral Regeneration of Stem Cel +- **VY8CRKCE** score=29 unknown=29 patterns=body_unknown=29|contrib=1|conflict=1|render_blocked=211 | Exploring the piezoelectric phenomenon: From polymers to human tissues and advan +- **UV6IVNUE** score=28 unknown=24 patterns=frontmatter_unknown=1|body_unknown=12|contrib=1|conflict=1 | Electrospinning Piezoelectric Fibers for Biocompatible Devices +- **YSBJVWTA** score=28 unknown=24 patterns=frontmatter_unknown=5|body_unknown=10|contrib=1|conflict=1 | PRIMER +- **WZLSE58A** score=28 unknown=28 patterns=body_unknown=22|render_blocked=97 | DIVERSE EFFECTS OF PULSED ELECTRICAL STIMULATION ON CELLS – WITH A FOCUS ON CHON +- **YII2HZEA** score=27 unknown=27 patterns=frontmatter_unknown=2|body_unknown=15|ref_unknown=1|conflict=1 | Slide-Ring Structured Stress-Electric Coupling Hydrogel Microspheres for Low-Los +- **WLMYX4XT** score=27 unknown=27 patterns=frontmatter_unknown=2|body_unknown=10|ref_unknown=1|conflict=1 | Print-and-Roll Hierarchically Structured Piezoelectric Scaffolds for Exercise-Dr +- **WDV72ZFQ** score=27 unknown=27 patterns=frontmatter_unknown=1|body_unknown=9|ref_unknown=3|conflict=1 | Metallic Nanoparticle Inks for 3D Printing of Electronics +- **VL5KKBZM** score=26 unknown=21 patterns=body_unknown=19|ethics=1|ref_gaps=33,34,35,37,38|render_blocked=79 | Acquired Acromion Compromise, Including Thinning and Fragmentation, Is Not Assoc +- **UVV6WCCV** score=26 unknown=20 patterns=frontmatter_unknown=1|body_unknown=15|conflict=1|ref_gaps=14,47,62,63,64 | Voltage-Dependent Calcium Channels in Chondrocytes: Roles in Health and Disease +- **TW2333LF** score=26 unknown=26 patterns=frontmatter_unknown=1|body_unknown=24|contrib=1|data_avail=1 | Current advances of biodegradable and biocompatible nanofiber-based materials fo +- **X5UHKKSM** score=25 unknown=25 patterns=frontmatter_unknown=1|body_unknown=18|conflict=1|render_blocked=284 | Electroactive Biomaterials Regulate the Electrophysiological Microenvironment to +- **VPGRTNJ7** score=25 unknown=25 patterns=frontmatter_unknown=1|body_unknown=15|conflict=1|render_blocked=103 | Accelerated Bone Healing via Electrical Stimulation +- **UT2WKEVN** score=25 unknown=25 patterns=frontmatter_unknown=1|body_unknown=21|render_blocked=104 | Novel Ultrathin Films Based on a Blend of PEG-b-PCL and PLLA and Doped with ZnO + + +*Report generated by scripts/dev/ocr_zone_role_audit.py* diff --git a/docs/superpowers/analysis/2026-07-02-reference-zone-ordering-analysis.md b/docs/superpowers/analysis/2026-07-02-reference-zone-ordering-analysis.md new file mode 100644 index 00000000..0d3c9ec7 --- /dev/null +++ b/docs/superpowers/analysis/2026-07-02-reference-zone-ordering-analysis.md @@ -0,0 +1,177 @@ +# Reference Zone & Ordering — Root Cause Analysis + +> **Date:** 2026-07-02 +> **Scope:** 50-paper scan → 14 with issues (28%) → deep-dive on all 14 + +--- + +## Summary of Findings + +| # | Pattern | Root Cause | Impact | Fix | +|---|---------|-----------|--------|-----| +| P0 | **Ref blocks silently dropped from fulltext** | `block_page_by_id` flat-dict collision in `ocr_render.py:1010-1022` | ~60% of all missing refs | Use `table.get("page")` instead of cross-page lookup | +| P1 | **Backmatter intrudes into ref section** | `_reorder_tail_run` Phase 4b (line 646-651) assigns unclaimed body_pool to ref_section | Content like "Address correspondence" appears between refs | Route body_pool in `tail_nonref_hold_zone` to backmatter, not refs | +| P2 | **skip_section_grouping places non_ref before refs** | Multi-column pages without ref_heading emit `non_ref + refs + backmatter` | "Received/Accepted" appears before trailing refs on same page | Minor — page-tied non_ref content naturally precedes trailing refs | +| P3 | **Page continuation markers classified as reference_item** | Narrow blocks ("13 of 18") matched `reference_like` style family | Pollutes ref count (5-6 per paper), doesn't lose real refs | Tighten reference_like gate for width < 200 && no citation content | +| P4 | **Unexplained ref loss (3 papers)** | 95FDVE4W ref 2, WV2FF4NV ref 9, 58UFL9UN refs 9,30,31 | 5 refs lost, mechanism unknown | Needs deeper render-loop debug | + +--- + +## P0: block_page_by_id Collision (CRITICAL) + +### Location +`paperforge/worker/ocr_render.py`, lines 1010-1022 (key construction) and 1438-1442 (consumption filter). + +### Root Cause +`block_page_by_id` is built as a **flat dict keyed by block_id alone** (a per-page integer, not globally unique): + +```python +# Line 1010-1015 — last-write-wins collision +block_page_by_id: dict[str | int, int | None] = {} +for block in structured_blocks: + bid = block.get("block_id") + page = block.get("page") + block_page_by_id[bid] = page # OVERWRITES earlier entries + block_page_by_id[str(bid)] = page +``` + +When `consumed_table_block_keys` is built (lines 1017-1022), each table's `consumed_block_ids` is paired with the **globally resolved page** from this dict — not the table's actual page: + +```python +for table in table_inventory.get("tables", []): + for block_id in table.get("consumed_block_ids", []): + page = block_page_by_id.get(block_id, table.get("page")) # BUG + consumed_table_block_keys.add((page, block_id)) +``` + +If the same integer block_id appears on a later page (e.g. a reference page), `block_page_by_id` returns the WRONG page for the table's consumed blocks. This causes the render loop's filter at line 1438-1442 to silently skip reference items whose block_id collides with a table's consumed block_id. + +### Confirmed Affected Refs + +| Paper | Missing Refs | Table Page | Ref Page | Colliding BlockIDs | +|-------|-------------|-----------|----------|-------------------| +| 37LK5T97 | 100, 101 | p12 (Table 4) | p20 | 2, 3 | +| B43QSAJP | 17, 18 | p5 | p22 | 5, 6 | +| 62LTMCI8 | 139-143 | p4/p5/p7/p8/p9/p11 | p18 | 2-6 | +| 4KCHGV2Z | 3-5, 7-8 | p2, p7 | p8 | 12-17 | +| 58UFL9UN | 120, 121 | p4 | p13 | 7, 8 | +| JQMRCEXY | 16-20 | p5, p6 | p9 | 4-8 | +| **Total** | **~20 refs** | | | | + +### Verifiable Effect +In all cases, the missing refs **exist** in structured blocks as `reference_item`, `zone=reference_zone`, `render_default=True`, `role_verification_status=ACCEPT`. They are in the reference zone artifact (`item_block_ids`). They reach `ordered_blocks`. They are silently dropped by the `consumed_table_block_keys` filter because `(page, block_id)` matches a table's consumed entry with the wrong page. + +### Fix +Replace line 1021 with the table's own page: + +```python +# Before: +page = block_page_by_id.get(block_id, table.get("page")) + +# After: +page = table.get("page") # consumed blocks exist on the table's page +``` + +The `consumed_block_ids` for a table (caption + asset) always live on the same page as the table. The cross-page lookup is unnecessary and introduces the collision. + +--- + +## P1: Backmatter Intrusion into Reference Zone + +### Location +`paperforge/worker/ocr_render.py`, `_reorder_tail_run` Phase 4b, lines 633-653. + +### Mechanism +On pages where `skip_section_grouping=True` (ref items present but no reference heading), body_pool blocks are classified. If a `body_paragraph` block doesn't match any backmatter section heading, it falls through to: + +```python +elif ref_section is not None and not _needs_synthetic_ref: + ref_section["bodies"].append(body) +``` + +Observed in 37LK5T97 page 20: "Address correspondence to:", "E-mail:", "Received/Accepted" are `body_paragraph` in `tail_nonref_hold_zone`. No backmatter heading on page 20 → they leak into `ref_section["bodies"]`. Since they have no numeric prefix, `_ref_number_sort_key` sorts them to the end. But on skip_section_grouping pages, `non_ref` content appears BEFORE `refs`, so the backmatter appears at the top of page 20. + +### Impact +Content ordering looks wrong — "Address correspondence" appears between ref 99 (page 19) and ref 100+ (page 20). The backmatter should be after all refs. + +### Fix Direction +Blocks with `zone=tail_nonref_hold_zone` should be routed to a separate backmatter section or emitted as `non_tail_pass` rather than falling into `body_pool` → `ref_section`. + +--- + +## P2: skip_section_grouping Non-ref Ordering + +### Location +`_reorder_tail_run` lines 524-532. + +### Mechanism +When skip_section_grouping=True: +```python +non_ref = [b for b in tail_blocks if b.get("role") not in ref_roles ...] +refs = [b for b in tail_blocks if b.get("role") in ref_roles] +refs.sort(key=_ref_number_sort_key) +return non_ref + refs + backmatter + fnotes, carried_ref, carried_backmatter +``` + +The output places ALL `non_ref` blocks BEFORE `refs`. On a page with mixed content (like backmatter continuation + refs), the backmatter appears first. + +### Impact +Minor — per-page ordering is technically correct for the reading flow, but when the page transition from refs (page X) to backmatter + refs (page X+1) happens, the backmatter appears to "jump in front" of the remaining refs. + +--- + +## P3: Page Continuation Markers as reference_item + +### Location +Style family assignment (`ocr_families.py`). + +### Manifestation +Blocks with narrow width (38-61px) containing text like "13 of 18" are classified as `style_family=reference_like` and assigned `role=reference_item`. They have NO actual reference content — they're page numbering artifacts. + +### Affected Papers +| Paper | Count | Sample | +|-------|-------|--------| +| 62LTMCI8 | 6 | "13 of 18" through "18 of 18" | +| TXMVULD7 | 5 | "12 of 16" through "16 of 16" | +| JQMRCEXY | 2 | "8 of 9", "9 of 9" | + +### Impact +Inflates reference item count by 5-6 per paper. Does NOT cause missing refs or ordering issues — the narrow items sort to the end by lexicographic order and don't displace real refs. + +### Fix Direction +In `ocr_families.py` or `ocr_scores.py`, add a gate: if block text matches `r"^\d+\s+of\s+\d+$"` OR bbox width < 100 AND text matches a page-marker pattern, reject `reference_like` classification. + +--- + +## P4: Unexplained Ref Loss (3 papers) + +These papers have ref blocks that exist in structured blocks with correct role but don't appear in fulltext, and the block_page_by_id collision doesn't apply (no table consumption hit). + +| Paper | Missing | Block | Page | Render Default | +|-------|---------|-------|------|---------------| +| 95FDVE4W | Ref 2 | bid=11, p16 | No collision | True | +| WV2FF4NV | Ref 9 | bid=39, p19 | block_page_by_id→p20 | True | +| 58UFL9UN | Refs 9,30,31 | bid=26,47,48, p10 | bid=26 resolves→p13 | True | + +WV2FF4NV and 58UFL9UN have block_page_by_id collision even without table consumption — the dict stores wrong page for that bid. This COULD affect other lookups in the render loop that use `block_page_by_id` (e.g. `consumed_caption_keys`). Needs further investigation. + +--- + +## Cross-Cutting: Column Layout Accuracy + +Analysis of tail_reading_order segments for 37LK5T97 page 20: +- **Segment 8** (col 0, left column): bid=0 (noise), refs 100-110 (bid=2-12) — correct +- **Segment 9** (col 1, right column): bid=1 (noise), refs 111-118 (bid=13-20), body_paragraph (bid=21-23) — correct + +All blocks are within their correct segments. No column assignment errors found. The remaining ColumnLayoutAccuracy agent data suggests other multi-column papers (B43QSAJP, 24A2QUAH) also have accurate column assignments. + +--- + +## Prioritized Fix List + +| Priority | Fix | Files | Lines | Effort | +|----------|-----|-------|-------|--------| +| **P0** | Use `table.get("page")` instead of `block_page_by_id` lookup | `ocr_render.py` | 1021 | 1 line | +| **P1** | Route `tail_nonref_hold_zone` body_paragraph away from ref_section | `ocr_render.py` | 571-579, 646-651 | ~5 lines | +| **P2** | Add page-marker gate to `reference_like` classification | `ocr_families.py` | ~330 | ~5 lines | +| **P3** | Investigate remaining unexplained losses (P4) | debug render loop | 1384-1600 | deeper | diff --git a/docs/superpowers/plans/2026-07-02-reference-detection-fix-plan.md b/docs/superpowers/plans/2026-07-02-reference-detection-fix-plan.md new file mode 100644 index 00000000..34fbad54 --- /dev/null +++ b/docs/superpowers/plans/2026-07-02-reference-detection-fix-plan.md @@ -0,0 +1,655 @@ +# Reference Detection Fix — Implementation Plan + +> **For agentic workers:** Four commits (sequential: 1 → 2/3/4 parallel or interleaved). +> +> **Prerequisite:** Spec at `docs/superpowers/specs/2026-07-02-reference-detection-fix-spec.md` + +**Goal:** Fix 5 reference-detection problems discovered in corpus audit (500 papers): +1. `(N)` parenthetical ref format not recognized (6% corpus) — **Commit 1** +2. Reference heading variants not detected ("References and Notes") — **Commit 2** +3. Cross-page ref role inconsistency (WNDJX4KB) — **Commit 3** +4. Wiley "References" heading absent from OCR — **No fix (OCR limitation)** +5. Rendering preservation — **Commit 4 (diagnostic, U746UJ7G already fixed by prior work)** + +**Architecture:** Commit 1 modifies 4 core files + tests. Commits 2/3/4 each modify one source file + its test; they can run in parallel after Commit 1. + +**Tech Stack:** Python 3.x, PaperForge OCR worker modules, pytest, no new runtime dependencies. + +--- + +## Commit 1: `(N)` Parenthetical Reference Support + +**Files:** +- Modify: `paperforge/worker/ocr_roles.py` +- Modify: `paperforge/worker/ocr_render.py` +- Modify: `paperforge/worker/ocr_reference_signals.py` +- Modify: `paperforge/worker/ocr_document.py` +- Modify: `tests/test_ocr_roles.py` +- Modify: `tests/test_ocr_render.py` +- Modify: `tests/test_ocr_document.py` +### Step 1: Read the current regex patterns + +Read these lines to confirm exact current code: +- `paperforge/worker/ocr_roles.py` line 72 (`_REFERENCE_PATTERN`) +- `paperforge/worker/ocr_roles.py` lines 1361-1369 (`_looks_like_reference` usage + `_BODY_ORDINAL_OPENINGS` guard) +- `paperforge/worker/ocr_render.py` line 488 (`_ref_number_sort_key`) +- `paperforge/worker/ocr_reference_signals.py` line 37 (`has_number_lead`) + +### Step 2: Write failing tests first + +Add to `tests/test_ocr_roles.py`: + +_PAREN_REF_TEXT = "(1) Li, T.; Shi, C.; Jin, F.; Yang, F.; Gu, L.; Wang, T.; Dong, W.; Feng, Z.-Q. Cell Activity Modulation and Its Specific Function in Load Bearing." +_SHORT_PAREN_HEADING = "(1) Introduction" + +def test_reference_pattern_accepts_long_paren_reference() -> None: + from paperforge.worker.ocr_roles import _looks_like_reference + assert _looks_like_reference(_PAREN_REF_TEXT) is True + +def test_reference_pattern_matches_short_paren_heading_pattern_only() -> None: + from paperforge.worker.ocr_roles import _looks_like_reference + # _looks_like_reference uses _REFERENCE_PATTERN which matches (N) + # regardless of length. Length guard is in assign_block_role, not here. + assert _looks_like_reference(_SHORT_PAREN_HEADING) is True + + +def test_assign_block_role_rejects_short_paren_heading() -> None: + from paperforge.worker.ocr_roles import assign_block_role + block = { + "raw_label": "text", + "text": "(1) Introduction", + "page": 3, + "bbox": [100, 100, 300, 130], + "page_width": 1200, + "page_height": 1600, + } + role = assign_block_role(block, page_blocks=[block]).role + assert role != "reference_item", f"Expected not reference_item, got {role}" +``` + +Add to `tests/test_ocr_document.py`: + +```python +def test_score_reference_entry_has_number_lead_paren() -> None: + from paperforge.worker.ocr_reference_signals import score_reference_entry + + result = score_reference_entry( + "(1) Smith AB, Jones CD. Journal Name. 2020;10(3):100-10." + ) + + assert result["signals"].get("number_lead") is True + assert result["family"] == "vancouver_structured_numbered" + + +def test_reference_completeness_accepts_parenthetical_numbers() -> None: + from paperforge.worker.ocr_document import _check_reference_completeness + + blocks = [ + {"role": "reference_item", "zone": "reference_zone", "text": "(1) A."}, + {"role": "reference_item", "zone": "reference_zone", "text": "(2) B."}, + {"role": "reference_item", "zone": "reference_zone", "text": "(3) C."}, + ] + + result = _check_reference_completeness(blocks) + + assert result["status"] == "OK" + assert result["expected_count"] == 3 + assert result["missing_numbers"] == [] +``` + +Add to `tests/test_ocr_render.py`: + +```python +def test_ref_number_sort_key_paren_format() -> None: + from paperforge.worker.ocr_render import _ref_number_sort_key + block = {"text": "(5) Smith J. Journal Name. 2020."} + key = _ref_number_sort_key(block) + assert key == (0, 5), f"Expected (0, 5), got {key}" + +def test_ref_number_sort_key_paren_handles_mixed_formats() -> None: + from paperforge.worker.ocr_render import _ref_number_sort_key + assert _ref_number_sort_key({"text": "(5) ..."}) == (0, 5) + assert _ref_number_sort_key({"text": "5. ..."}) == (0, 5) + assert _ref_number_sort_key({"text": "[5] ..."}) == (0, 5) +``` +### Step 3: Run the tests — expect failures + +```bash +pytest tests/test_ocr_roles.py::test_reference_pattern_accepts_long_paren_reference \ + tests/test_ocr_roles.py::test_reference_pattern_matches_short_paren_heading_pattern_only \ + tests/test_ocr_roles.py::test_assign_block_role_rejects_short_paren_heading \ + tests/test_ocr_render.py::test_ref_number_sort_key_paren_format \ + tests/test_ocr_render.py::test_ref_number_sort_key_paren_handles_mixed_formats \ + tests/test_ocr_document.py::test_score_reference_entry_has_number_lead_paren \ + tests/test_ocr_document.py::test_reference_completeness_accepts_parenthetical_numbers -v +``` + +### Step 4: Implement `_REFERENCE_PATTERN` fix + +In `paperforge/worker/ocr_roles.py`, find `_REFERENCE_PATTERN` (around line 72). Add `\(\d+\)\s` as the first alternative: + +```python +_REFERENCE_PATTERN = re.compile( + r"^\s*(?:\(\d+\)\s|\d+\.\s|[A-Z][A-Za-z'’\-]+\s+et al\.\s*\(\d{4}[a-z]?\)|\([A-Z][A-Za-z'’\-]+\s+et al\.,\s*\d{4}[a-z]?\))", +) +``` + +### Step 5: Add length guard in `assign_block_role()` + +Find the `_looks_like_reference` usage around line 1361-1369. Insert the `_PAREN_REF_PREFIX` compile before the function (top of file or local) and add the length guard: + +Add at module level (with other pattern compiles): +```python +_PAREN_REF_PREFIX = re.compile(r"^\s*\(\d+\)\s*") +``` + +Modify the guard block (around line 1362-1368): +```python + # text with reference-like pattern + if _looks_like_reference(text): + first_word = text.strip().split(",")[0].strip().lower() + if first_word not in _BODY_ORDINAL_OPENINGS: + # Length guard: (N) prefix with very short body → likely a heading, not a ref + stripped = _PAREN_REF_PREFIX.sub("", text).strip() + if text.lstrip().startswith("(") and len(stripped) < 25: + pass # skip — short (N) text is not a reference item + else: + return RoleAssignment( + role="reference_item", + confidence=0.6, + evidence=[f"reference-like pattern: {text[:60]}"], + ) +``` + +### Step 6: Implement `_ref_number_sort_key` fix + +In `paperforge/worker/ocr_render.py`, find `_ref_number_sort_key` (around line 488). Change the regex and return: + +```python +def _ref_number_sort_key(block: dict) -> tuple: + text = str(block.get("text") or block.get("block_content") or "") + m = re.match(r"^\s*(?:(\d+)[\.\)]|\[(\d+)\]|\((\d+)\))", text) + if m: + num = m.group(1) or m.group(2) or m.group(3) + return (0, int(num)) + return (1, text) +``` + +### Step 7: Implement `has_number_lead` fix + +In `paperforge/worker/ocr_reference_signals.py`, find `has_number_lead` (around line 37). Change: + +```python +has_number_lead = bool( + re.match(r"^\s*(\(\d+\)|\[\d+\]|\d+[\.)]?)(\s+|$)", text) +) +``` + +Also expose it in the return dict so the test can check it directly. Look for the return dict and add if absent: + +```python +return { + "family": family, + "confidence": confidence, + "signals": { + "author_signature": has_author_signature, + "year_signature": has_year, + "volume_issue_pages_signature": has_vol_pages, + "online_marker_signature": has_online, + "journal_lexicon_match": journal_match, + "number_lead": has_number_lead, + }, +} +``` + +### Step 7.5: Implement `_check_reference_completeness` fix + +Find `_check_reference_completeness()` in `paperforge/worker/ocr_document.py` at line 3221. +Add parenthetical pattern BEFORE the bracket pattern at line 3237: + +```python +text = (block.get("text") or "").strip() +# Try parenthetical pattern: (1) +m = _re.match(r"^\s*\((\d+)\)", text) +if m: + numbers.append(int(m.group(1))) + continue +# Try bracket pattern: [1] +m = _re.match(r"^\s*\[(\d+)\]", text) # existing, unchanged +... +``` + +This prevents completeness false positives for `(N)` format papers. + + +### Step 8: Run tests — expect pass + +```bash +pytest tests/test_ocr_roles.py::test_reference_pattern_accepts_long_paren_reference \ + tests/test_ocr_roles.py::test_reference_pattern_matches_short_paren_heading_pattern_only \ + tests/test_ocr_roles.py::test_assign_block_role_rejects_short_paren_heading \ + tests/test_ocr_render.py::test_ref_number_sort_key_paren_format \ + tests/test_ocr_render.py::test_ref_number_sort_key_paren_handles_mixed_formats \ + tests/test_ocr_document.py::test_score_reference_entry_has_number_lead_paren -v +``` + +Expected: 6 passed. + +### Step 9: Run full existing test suite + +```bash +pytest tests/test_ocr_roles.py tests/test_ocr_render.py tests/test_ocr_document.py tests/test_ocr_families.py -q +``` + +Expected: all existing tests still pass (count unchanged for unrelated files). +### Step 10: Commit + +```bash +git add paperforge/worker/ocr_roles.py paperforge/worker/ocr_render.py paperforge/worker/ocr_reference_signals.py paperforge/worker/ocr_document.py tests/test_ocr_roles.py tests/test_ocr_render.py tests/test_ocr_document.py +git commit -m "fix: support parenthetical (N) reference number format + +Add (N) prefix to 4 regex locations: +- _REFERENCE_PATTERN: recognize (1) as reference start +- _ref_number_sort_key: extract number from (N) for sort +- has_number_lead in score_reference_entry: detect (N) as numbered ref +- _check_reference_completeness: count (N) refs in completeness check + +Add length guard in assign_block_role: (N) prefix + text < 25 chars +is rejected (prevents '(1) Introduction' false positive). +Corpus: 30/500 papers use (N) format, previously all misclassified." +``` + +--- + +## Commit 2: Reference Heading Variant Expansion + +**Files:** +- Modify: `paperforge/worker/ocr_roles.py` +- Modify: `tests/test_ocr_roles.py` + +### Step 1: Read the current heading assignment code + +Read `paperforge/worker/ocr_roles.py` and find: +- Where `paragraph_title` raw_label is processed and assigned to `section_heading` / `subsection_heading` +- The entry point for `assign_block_role` (the function that reads `raw_label` and returns a `RoleAssignment`) + +### Step 2: Add the heading detection helper + +Add to `paperforge/worker/ocr_roles.py` (near the top with other pattern compiles, or just before `assign_block_role`): + +```python +_REFERENCE_HEADING_PATTERN = re.compile( + r"^(?:" + r"references?" + r"|references?\s+and\s+(?:notes?|further\s+reading)" + r"|bibliography" + r"|cited\s+references?" + r")$", + re.IGNORECASE, +) + + +def _normalize_heading_text(text: str) -> str: + """Strip leader dots, trailing page numbers, and trailing colon. + + 'References ..... 42' → 'References' + 'References:' → 'References' + 'References and Notes ..... 3054' → 'References and Notes' + """ + text = text.strip().rstrip(":") + text = re.sub(r"\.{2,}\s*\d+\s*$", "", text) + text = re.sub(r"\s+\d+\s*$", "", text) + return text.strip() + + +def _is_reference_heading_text(text: str) -> bool: + """Check if text represents a reference section heading. + Uses fullmatch to prevent false positives like 'References in this article'. + """ + return bool(_REFERENCE_HEADING_PATTERN.fullmatch(_normalize_heading_text(text))) +``` + +### Step 3: Integrate into `assign_block_role()` + +Find the point in `assign_block_role()` where heading-like blocks (`raw_label == "paragraph_title"` or similar) are about to be assigned a generic heading role. Insert BEFORE that assignment: + +```python + # Reference heading detection — must run before generic heading assignment + heading_text = text.strip() + if _is_reference_heading_text(heading_text): + return RoleAssignment( + role="reference_heading", + confidence=0.85, + evidence=[f"reference heading text match: {heading_text[:60]}"], + ) +``` + +The exact insertion point depends on the function structure. Search for where `paragraph_title` raw_label is handled and add the check before the standard heading role assignment. + +### Step 4: Write tests + +Add to `tests/test_ocr_roles.py`: + +```python +import pytest + + +@pytest.mark.parametrize("text", [ + "References", + "Reference", + "REFERENCES", + "References and Notes", + "References and Notes ..... 42", + "Bibliography", + "Cited References", +]) +def test_reference_heading_variants(text: str) -> None: + from paperforge.worker.ocr_roles import _is_reference_heading_text + assert _is_reference_heading_text(text), f"Expected match: {text!r}" + + +@pytest.mark.parametrize("text", [ + "References in this article", + "Reference values", + "Further reading", + "References and results", +]) +## Commit 3: Preserve heading-page reference_content after partition fallback (WNDJX4KB) + +**Files:** +- Modify: `paperforge/worker/ocr_document.py` (post-partition guard in `normalize_document_structure`) +- Modify: `tests/test_ocr_document.py` + +**Status: EXECUTABLE** — root cause confirmed. Test must verify _decision_log. + +### Root Cause (Trace-Confirmed) + +1. `_partition_by_reference_zone` excludes heading-page refs from the partition. +2. `_clear_partition_zones` + `_apply_zone_labels` then strip their `reference_zone` label. +3. Final role falls to `body_paragraph` because no partition override applies. + +The fix is NOT in `_normalize_reference_roles_from_partition` (that only promotes IN-partition blocks). It's a post-partition fallback in `normalize_document_structure`. + +### Step 1: Read the partition boundary logic + +Read `_partition_by_reference_zone` in `ocr_document.py` to understand how heading-page blocks get excluded. Read `normalize_document_structure` to find the right insertion point: after `_normalize_reference_roles_from_partition` returns, before `_clear_partition_zones`. + +### Step 2: Write integration test that would fail without the fix + +The test must prove the fix actually fires — not just assert correct roles on hand-crafted blocks. + +Add to `tests/test_ocr_document.py`: + +```python +def test_normalize_document_structure_preserves_heading_page_reference_items() -> None: + """Heading-page reference_item blocks excluded from partition must be + restored by fallback guard. Verifies _decision_log for partition_fallback.""" + from paperforge.worker.ocr_document import normalize_document_structure + + blocks = [ + {"page": 1, "role": "reference_heading", "raw_label": "paragraph_title", + "text": "References", "bbox": [100, 100, 200, 120], + "page_width": 1200, "page_height": 1600, "block_id": "h1"}, + {"page": 1, "role": "reference_item", "seed_role": "reference_item", + "raw_label": "reference_content", + "text": "1. Author A. Journal. 2020.", + "bbox": [100, 130, 500, 150], + "page_width": 1200, "page_height": 1600, "block_id": "r1"}, + {"page": 2, "role": "reference_item", "seed_role": "reference_item", + "raw_label": "reference_content", + "text": "2. Author B. Journal. 2021.", + "bbox": [100, 130, 500, 150], + "page_width": 1200, "page_height": 1600, "block_id": "r2"}, + ] + + doc, normalized = normalize_document_structure(blocks) + + for b in normalized: + if b.get("block_id") in ("r1", "r2"): + assert b.get("role") == "reference_item", \ + f"Block {b['block_id']} demoted to {b.get('role')}" + dl = b.get("_decision_log", []) + fallback_entries = [ + d for d in (dl if isinstance(dl, list) else []) + if isinstance(d, dict) and d.get("stage") == "partition_fallback" + ] + assert any( + d.get("stage") == "partition_fallback" + for d in (dl if isinstance(dl, list) else []) + if isinstance(d, dict) + ), f"Block {b['block_id']} did not trigger partition_fallback — test would pass without fix" +``` + +### Step 3: Add post-partition fallback guard in `normalize_document_structure()` + +Insert AFTER `_normalize_reference_roles_from_partition(temp_blocks, all_blocks)` returns and BEFORE `_clear_partition_zones(temp_blocks)`: + +```python +# Post-partition fallback: restore reference_item for blocks that OCR +# explicitly identified as reference content but were excluded from the +# reference partition boundary (WNDJX4KB pattern — heading-page refs). +for block in temp_blocks: + zone = str(block.get("zone") or "") + seed = str(block.get("seed_role") or "") + raw = str(block.get("raw_label") or block.get("block_label") or "") + if block.get("role") == "body_paragraph" and "reference" in zone: + if seed == "reference_item" or raw == "reference_content": + block["role"] = "reference_item" + _record_decision( + block, + stage="partition_fallback", + old_role="body_paragraph", + new_role="reference_item", + reason="reference_content block outside partition, restored from seed_role", + ) +``` + +Search for `_record_decision` or `record_decision` in the file to get the exact function name. + +### Step 4: Verify + +```bash +pytest tests/test_ocr_document.py::test_normalize_document_structure_preserves_heading_page_reference_items -v +python scripts/dev/ocr_rebuild_paper.py WNDJX4KB +# Check blocks 1-6 have role=reference_item AND partition_fallback log +python -c " +import json, re +with open('D:/L/OB/Literature-hub/System/PaperForge/ocr/WNDJX4KB/structure/blocks.structured.jsonl', encoding='utf-8') as f: + blocks = [json.loads(l) for l in f if l.strip()] +for b in blocks: + t = str(b.get('text','') or b.get('block_content','')) + m = re.match(r'^\s*([1-6])[.\)]\s', t) + if m: + dl = b.get('_decision_log', []) + has_fb = any(d.get('stage') == 'partition_fallback' for d in (dl if isinstance(dl, list) else []) if isinstance(d, dict)) + print(f'Ref {m.group(1)}: role={b.get(\"role\")} fallback={has_fb}') +" +``` + +### Step 5: Run full suite + +```bash +pytest tests/test_ocr_document.py tests/test_ocr_render.py tests/test_ocr_families.py -q +``` + +### Step 6: Commit + +```bash +git add paperforge/worker/ocr_document.py tests/test_ocr_document.py +git commit -m "fix: preserve heading-page reference_content after partition fallback + +Reference partition can exclude reference_content blocks on the same page +as the reference heading. After partition normalization, restore blocks +whose seed_role/raw_label and zone still identify them as reference items. +Fixes WNDJX4KB refs 1-6 demoted to body_paragraph." +``` + +## Commit 4: Reference Rendering Preservation + Collision Logging (Diagnostic) + +**Files:** +- Modify: `paperforge/worker/ocr_render.py` +- Modify: `tests/test_ocr_render.py` + +**Type: DIAGNOSTIC** — does not fix U746UJ7G (refs already rendered correctly since P0-P4 layout work). +Just add safety net: preservation invariant + duplicate-number collision logging. + +**Depends on:** Commit 1 (`_ref_number_sort_key` update) + +### Root Cause + +U746UJ7G **no longer has a problem** — rebuild after P0-P4 + layout robustness commits shows +all 46 refs (40, 41, 43 included) are present in both structured blocks and fulltext. +No numbering collision found. + +Commit 4 exists only as a diagnostic safety net: if future papers have duplicate-numbered refs, +we log the collision and check preservation invariants. + +=== CRITICAL: Insertion Position === +The dedup/collision code MUST go between sort and extend: + +```python +if ref_section.get("bodies"): + ref_section["bodies"].sort(key=_ref_number_sort_key) + # ← COLLISION LOGGING GOES HERE (after sort, before extend) + result.extend(ref_section["bodies"]) +``` + +If placed after `result.extend(ref_section["bodies"])`, the modification to `ref_section["bodies"]` +does NOT affect the output — it's already been emitted. + +### Step 1: Add preservation invariant tests + +Add to `tests/test_ocr_render.py`: + +```python +def test_reorder_tail_run_preserves_all_reference_items() -> None: + from paperforge.worker.ocr_render import _reorder_tail_run + + ref_heading = {"role": "reference_heading", "text": "References", "bbox": [100, 100, 200, 120]} + refs = [ + {"role": "reference_item", "text": f"{i}. Entry {i}.", "bbox": [100, 120 + i * 20, 500, 140 + i * 20]} + for i in range(1, 6) + ] + tail_blocks = [ref_heading, *refs] + + ordered, _, _ = _reorder_tail_run(tail_blocks, None, None, page_width=1200) + + before = {id(b) for b in tail_blocks if b.get("role") == "reference_item"} + after = {id(b) for b in ordered if b.get("role") == "reference_item"} + assert before == after, f"Lost refs: {before - after}" + + +def test_reorder_tail_run_preserves_duplicate_numbered_refs() -> None: + """Two different refs with the same number must BOTH survive (no dedup by number).""" + from paperforge.worker.ocr_render import _reorder_tail_run + + heading = {"role": "reference_heading", "text": "References", "bbox": [100, 100, 200, 120]} + ref42a = {"role": "reference_item", "text": "42. Rhee C, Wang R...", "bbox": [100, 200, 500, 220]} + ref42b = {"role": "reference_item", "text": "42. Baghdadi JD, Brook RH...", "bbox": [100, 220, 500, 240]} + ref43 = {"role": "reference_item", "text": "43. Baghdadi JD, Wong MD...", "bbox": [100, 240, 500, 260]} + + ordered, _, _ = _reorder_tail_run([heading, ref42a, ref42b, ref43], None, None, page_width=1200) + + before = {id(b) for b in [ref42a, ref42b, ref43]} + after = {id(b) for b in ordered if b.get("role") == "reference_item"} + assert before == after, f"Lost refs: {before - after}" +``` + +### Step 2: Add collision logging only (NO exact-text dedup) + +In `_reorder_tail_run()`, locate the sort-then-extend block and insert logging between them: + +```python +if ref_section.get("bodies"): + ref_section["bodies"].sort(key=_ref_number_sort_key) + + # Collision diagnostic: log duplicate ref numbers. + # Do NOT drop by number — different refs sharing a number is an OCR + # numbering error, not duplicate content. Dropping loses valid refs. + seen_numbers: set[int] = set() + for block in ref_section["bodies"]: + key = _ref_number_sort_key(block) + if key[0] == 0: + num = key[1] + if num in seen_numbers: + import logging + logging.warning(f"Duplicate ref number {num}: '{str(block.get('text',''))[:60]}'") + seen_numbers.add(num) + + result.extend(ref_section["bodies"]) +``` + +### Step 3: Verify + +```bash +pytest tests/test_ocr_render.py::test_reorder_tail_run_preserves_all_reference_items \ + tests/test_ocr_render.py::test_reorder_tail_run_preserves_duplicate_numbered_refs -v +python scripts/dev/ocr_rebuild_paper.py U746UJ7G +python -c " +import re +t = open('D:/L/OB/Literature-hub/System/PaperForge/ocr/U746UJ7G/fulltext.md', encoding='utf-8').read() +for n in [40, 41, 42, 43]: + found = bool(re.search(rf'^{n}\. ', t, re.MULTILINE)) + print(f'Ref {n}: {\"OK\" if found else \"MISSING\"}') +" +``` + +### Step 4: Run full suite + +```bash +pytest tests/test_ocr_document.py tests/test_ocr_render.py tests/test_ocr_families.py -q +``` + +### Step 5: Commit + +```bash +git add paperforge/worker/ocr_render.py tests/test_ocr_render.py +git commit -m "fix: add reference rendering preservation invariant + collision logging + +Add preservation invariant: all reference_item blocks survive rendering +(including duplicate-numbered refs — do NOT dedup by number). +Add collision logging for duplicate ref numbers only (no exact-text dedup). +Diagnostic only: U746UJ7G already fixed by earlier P0-P4 layout work." +``` +## No Fix: Track 4 Wiley Heading + +**Status: LIMITATION** — 97M7HFCD and 2HEUD5P9 confirmed "References" heading text not in PaddleOCR output. No pipeline code fix. + +--- + +## Conditional: 4AG67PBH Bio Split (Post-Commit-2+3) + +Re-test after Commits 2 and 3: + +```bash +python scripts/dev/ocr_rebuild_paper.py 4AG67PBH +python -c " +from pathlib import Path +import json +with open(Path('D:/L/OB/Literature-hub/System/PaperForge/ocr/4AG67PBH/structure/blocks.structured.jsonl'), encoding='utf-8') as f: + blocks = [json.loads(l) for l in f if l.strip()] +bio_in_ref = [ + b for b in blocks + if 'reference' in str(b.get('zone','')) + and 'Ph.D.' in str(b.get('text','') or b.get('block_content','')) +] +print(f'Bios still in reference_zone: {len(bio_in_ref)}') +" +``` + +If > 0: add post-reference backmatter split rule. +If == 0: no further action. + +--- +## Summary + +| # | Type | Description | Depends on | +|---|------|-------------|-----------| +| 1 | **Commit** | `(N)` reference format (4 regex + length guard) | — | +| 2 | **Commit** | Reference heading variants (fullmatch regex) | After 1 (same file) | +| 3 | **Commit** | Preserve heading-page reference_content after partition | After 1 (same file) | +| 4 | **Commit** | Reference rendering preservation + collision logging (Diagnostic) | After 1 (uses _ref_number_sort_key) | +| — | **No fix** | Wiley heading — OCR limitation (Track 4) | — | +| 5 | **Conditional** | 4AG67PBH bio split (re-test after 2+3) | After 2+3 | + +**Execution order:** 1 → 2/3/4 can run in parallel after 1 (different files, all depend on 1) → 5. diff --git a/docs/superpowers/plans/2026-07-02-reference-zone-ordering-fix-plan.md b/docs/superpowers/plans/2026-07-02-reference-zone-ordering-fix-plan.md new file mode 100644 index 00000000..42cf66b1 --- /dev/null +++ b/docs/superpowers/plans/2026-07-02-reference-zone-ordering-fix-plan.md @@ -0,0 +1,437 @@ +# Implementation Plan: Reference Zone Fixes + +> **Based on:** `docs/superpowers/specs/2026-07-02-reference-zone-ordering-fix-spec.md` +> **Commits:** 5 sequential, independently verifiable +> **Target:** 9 papers verified clean after all commits +> **Tests:** 12 unit tests (8 positive + 4 anti-regression) + +--- + +## Commit 1: P0 — Table Consumed Key Page Collision + +### Files +- `paperforge/worker/ocr_render.py` — consumed_table_block_keys construction (lines ~1010-1022) + +### Changes + +**1.1 — Add `_add_consumed_key` helper** before `render_fulltext_markdown` or as module-level function: + +```python +def _add_consumed_key( + keys: set[tuple[int | None, str | int]], + page: int | None, + block_id: str | int, +) -> None: + if block_id is None or block_id == "": + return + keys.add((page, block_id)) + keys.add((page, str(block_id))) +``` + +**1.2 — Rewrite consumed_table_block_keys construction** in `render_fulltext_markdown()`. + +Remove lines that build `block_page_by_id` (the flat dict). Replace the table-consumption loop with: + +```python +consumed_table_block_keys: set[tuple[int | None, str | int]] = set() + +def _add_and_remember(page, block_id): + if block_id is None or block_id == "": + return + _add_consumed_key(consumed_table_block_keys, page, block_id) + keyed_bid_strs.add(str(block_id)) + +for table in table_inventory.get("tables", []): + table_page = table.get("page") + keyed_bid_strs: set[str] = set() + + # Caption block — always on table's page + _add_and_remember(table_page, table.get("caption_block_id")) + + # Asset segments — each has its own page (caption ±1) + for seg in table.get("segments", []): + _add_and_remember(seg.get("page"), seg.get("asset_block_id")) + + # Note blocks on same page + for bid in table.get("note_block_ids", []): + _add_and_remember(table_page, bid) + + # Bridge/continuation blocks — same page as caption + for bid in table.get("bridge_block_ids", []): + _add_and_remember(table_page, bid) + + # Legacy fallback: only ids NOT already page-keyed + for bid in table.get("consumed_block_ids", []): + if bid is None or bid == "": + continue + if str(bid) in keyed_bid_strs: + continue + _add_consumed_key(consumed_table_block_keys, table_page, bid) +``` + +**1.3 — Cleanup:** If `block_page_by_id` is no longer used elsewhere in the function, remove its construction loop. If still used (e.g. for `_block_page_map` or `_block_text_by_bid`), keep it but do NOT use it for consumed key resolution. + +### Verification + +```bash +# 1. Parse check +python -c "import ast; ast.parse(open('paperforge/worker/ocr_render.py').read()); print('OK')" + +# 2. Unit test +python -m pytest tests/test_ocr_render.py::test_table_consumed_block_ids_do_not_drop_same_id_reference_on_later_page -v +python -m pytest tests/test_ocr_render.py::test_cross_page_table_asset_id_does_not_consume_same_id_on_caption_page -v + +# 3. Paper regression: rebuild 37LK5T97, check refs 100-101 appear +python scripts/dev/ocr_rebuild_paper.py 37LK5T97 +grep "100\. Lin" /path/to/ocr/37LK5T97/fulltext.md + +# 4. Repeat for B43QSAJP (refs 17-18), 62LTMCI8 (139-143), 4KCHGV2Z (3-5,7-8), +# 58UFL9UN (120-121), JQMRCEXY (16-20) +``` + +--- + +## Commit 2: P1 — `skip_section_grouping` Ordering + +### Files +- `paperforge/worker/ocr_render.py` — `_reorder_tail_run()` skip_section_grouping branch (lines ~524-532) + +### Changes + +**2.1 — Add `_is_tail_backmatter_continuation` helper** in `ocr_render.py`: + +```python +_TAIL_BACKMATTER_CONTINUATION_PATTERN = re.compile( + r"^(?:address correspondence|correspondence|e-?mail|email|" + r"received|accepted|published|available online|" + r"author contributions?|conflicts? of interest|funding|" + r"acknowledg(?:e)?ments?)\b", + re.IGNORECASE, +) + +def _is_tail_backmatter_continuation(block: dict) -> bool: + zone = str(block.get("zone") or "") + if zone == "tail_nonref_hold_zone": + return True + text = str(block.get("text") or block.get("block_content") or "").strip() + return bool(_TAIL_BACKMATTER_CONTINUATION_PATTERN.match(text)) +``` + +**2.2 — Rewrite `skip_section_grouping` branch:** + +```python +if skip_section_grouping: + ref_roles = frozenset({"reference_heading", "reference_item", "reference_body"}) + backmatter_roles = frozenset({ + "backmatter_body", + "backmatter_heading", + "backmatter_boundary_heading", + }) + + non_ref_all = [ + b for b in tail_blocks + if b.get("role") not in ref_roles + and b.get("role") not in backmatter_roles + and b.get("role") != "footnote" + ] + + refs = [b for b in tail_blocks if b.get("role") in ref_roles] + refs.sort(key=_ref_number_sort_key) + + backmatter = [b for b in tail_blocks if b.get("role") in backmatter_roles] + fnotes = [b for b in tail_blocks if b.get("role") == "footnote"] + + tail_backmatter = [b for b in non_ref_all if _is_tail_backmatter_continuation(b)] + ordinary_non_ref = [b for b in non_ref_all if not _is_tail_backmatter_continuation(b)] + + return (ordinary_non_ref + refs + backmatter + tail_backmatter + fnotes, + carried_ref, carried_backmatter) +``` + +### Verification + +```bash +# Unit tests +python -m pytest tests/test_ocr_render.py::test_skip_section_grouping_places_tail_nonref_after_refs -v +python -m pytest tests/test_ocr_render.py::test_skip_section_grouping_keeps_ordinary_nonref_before_refs -v +python -m pytest tests/test_ocr_render.py::test_real_backmatter_heading_still_attaches_its_own_body -v + +# Paper: 37LK5T97 page 20 — "Address correspondence" must appear after refs 100-118 +python scripts/dev/ocr_rebuild_paper.py 37LK5T97 +# Check that refs 100-118 appear before "Address correspondence" in fulltext +``` +```python +tail_backmatter_blocks: list[dict] = [] + +# Phase 4b — geometric body attachment +for body in body_pool: + idx = _find_owning_heading(body, backmatter_sections, page_width) + if idx is not None: + backmatter_sections[idx]["bodies"].append(body) + continue + + if _is_tail_backmatter_continuation(body): + tail_backmatter_blocks.append(body) + continue + + if carried_backmatter is not None: + bbox = body.get("bbox") or body.get("block_bbox") + if bbox and len(bbox) >= 4: + body_top = bbox[1] + if (first_local_anchor_top is None or body_top < first_local_anchor_top) and ( + not ref_heading or body_top < ref_bottom + ): + carried_bodies.append(body) + continue + + if ref_section is not None and not _needs_synthetic_ref: + if ref_section is carried_ref: + ref_section["bodies"].append(body) + orphan_blocks.append(body) + else: + ref_section["bodies"].append(body) + else: + orphan_blocks.append(body) +``` + tail_backmatter_blocks.append(body) + continue + + +**3.2 — Update emit order** (Phase 5, after `ref_section` emission): + +```python +result.extend(non_tail_pass) +result.extend(carried_bodies) +# ... backmatter sections ... +# ... ref section ... +result.extend(tail_backmatter_blocks) # ← NEW: between refs and footnotes +result.extend(footnote_blocks) +result.extend(orphan_blocks) +``` + +## Commit 3: P2 — Phase 4b Tail Nonref Guard + +### Files +- `paperforge/worker/ocr_render.py` — `_reorder_tail_run()` Phase 4b body_pool loop (lines ~633-653) + +### Changes + +(see code block above — guard after `_find_owning_heading()`, `tail_backmatter_blocks`, emit between refs and footnotes) + + +### Verification + +```bash +# Unit tests +python -m pytest tests/test_ocr_render.py::test_phase_4b_does_not_swallow_tail_nonref_into_ref_section -v +python -m pytest tests/test_ocr_render.py::test_funding_body_still_attaches_to_funding_heading -v + +# Regression: 37LK5T97 still clean after commit 2 + commit 3 +``` + +--- + +## Commit 4: P3 — Page Continuation Marker + +### Files +- `paperforge/worker/ocr_families.py` — 3 entry points + +### Changes + +**4.1 — Add helper** at module level in `ocr_families.py`: + +```python +_PAGE_CONTINUATION_MARKER_PATTERN = re.compile( + r"^(?:page\s*)?\d{1,4}\s*(?:[\.\-–—]?\s+of\s+|/)\s*\d{1,4}$", + re.IGNORECASE, +) + +def _looks_like_page_continuation_marker(block: dict) -> bool: + text = str(block.get("text") or block.get("block_content") or "").strip() + if not _PAGE_CONTINUATION_MARKER_PATTERN.match(text): + return False + + bbox = block.get("bbox") or block.get("block_bbox") or [] + width = float(bbox[2]) - float(bbox[0]) if len(bbox) >= 4 else None + layout_sig = block.get("layout_signature") or {} + if layout_sig.get("width") is not None: + width = float(layout_sig["width"]) + + if width is not None: + return width < 180 + return len(text.split()) <= 3 +``` + +**4.2 — Gate at three entry points:** + +```python +# In _is_reference_family_candidate(), early return: +if _looks_like_page_continuation_marker(block): + return False + +# In _reference_anchor_matches_block(), early return: +if _looks_like_page_continuation_marker(block): + return False + +# In _has_reference_text_structure(), early return: +if _looks_like_page_continuation_marker(block): + return False +``` + +### Verification + +```bash +# Unit tests +python -m pytest tests/test_ocr_families.py::test_page_continuation_marker_is_not_reference -v +python -m pytest tests/test_ocr_families.py::test_real_reference_is_still_reference -v + +# Paper rebuild +python scripts/dev/ocr_rebuild_paper.py 62LTMCI8 +# Check "13 of 18" blocks no longer have role=reference_item + +# Also check TXMVULD7, JQMRCEXY +``` + +--- + +## Commit 5: P4 — Same-Page Ref Blocks Before Reference Heading + +### Files +- `paperforge/worker/ocr_render.py` — `_order_tail_blocks()` AND non-tail page path + +### Changes + +**5.1 — Add helper** in `ocr_render.py`: + +```python +def _force_reference_heading_before_same_page_refs(page_blocks: list[dict]) -> list[dict]: + """Reorder page blocks so reference_item/reference_body always follow + the first reference_heading on the same page. Non-ref blocks are unchanged.""" + headings = [b for b in page_blocks if b.get("role") == "reference_heading"] + if not headings: + return page_blocks + + ref_roles = {"reference_item", "reference_body"} + refs = [b for b in page_blocks if b.get("role") in ref_roles] + if not refs: + return page_blocks + + first_heading = headings[0] + heading_idx = page_blocks.index(first_heading) + + before = [b for b in page_blocks[:heading_idx] if b.get("role") not in ref_roles] + after = [b for b in page_blocks[heading_idx + 1:] if b.get("role") not in ref_roles] + + return before + [first_heading] + sorted(refs, key=_ref_number_sort_key) + after +``` + +**5.2 — Fix early return in `_order_tail_blocks()`** for non-tail pages with ref heading: + +Current code returns early when no tail pages detected, skipping pages with `reference_heading` + `reference_item` that don't qualify as tail pages. The fix replaces the early return: + +```python +# Before: +if not tail_pages: + return blocks + +# After: +if not tail_pages: + result: list[dict] = [] + by_page: dict[int, list[dict]] = {} + for block in blocks: + p = block.get("page") + if p is None: + result.append(block) + else: + by_page.setdefault(p, []).append(block) + for page in sorted(by_page): + result.extend(_force_reference_heading_before_same_page_refs(by_page[page])) + return result +``` + +**5.3 — Apply helper in tail page path:** + +```python +if page in tail_pages: + pw = page_widths.get(page, 1200) + sorted_blocks = _sort_blocks_by_column(page_blocks, pw) + sorted_blocks = _force_reference_heading_before_same_page_refs(sorted_blocks) # ← NEW + ... +``` + +**5.4 — Update `_page_has_ref_items`** to also check `reference_body`: + +```python +# Before: +_page_has_ref_items = any(b.get("role") == "reference_item" for b in sorted_blocks) + +# After: +_page_has_ref_items = any(b.get("role") in {"reference_item", "reference_body"} for b in sorted_blocks) +``` + + +### Verification + +```bash +# Unit tests +python -m pytest tests/test_ocr_render.py::test_refs_on_heading_page_are_rendered_after_heading -v +python -m pytest tests/test_ocr_render.py::test_non_ref_blocks_not_moved_by_guard -v + +# Paper rebuild +python scripts/dev/ocr_rebuild_paper.py 95FDVE4W +grep "2\. Bedi" /path/to/ocr/95FDVE4W/fulltext.md +# Ref 2 must appear after "## References" heading + +# Also verify WV2FF4NV (ref 9), 58UFL9UN (refs 9, 30, 31) +``` + +--- + +## Full Regression + +After all 5 commits, run: + +```bash +# 1. All unit tests +python -m pytest tests/ -q + +# 2. All 9 regression papers +for key in 37LK5T97 B43QSAJP 62LTMCI8 4KCHGV2Z 58UFL9UN JQMRCEXY TXMVULD7 95FDVE4W WV2FF4NV; do + python scripts/dev/ocr_rebuild_paper.py $key +done + +# 3. Run reference-zone audit +python scripts/dev/ocr_reference_zone_audit.py --limit=50 +# Expect: 0 papers with ref ordering issues +``` + +**Unit test checklist (12 total):** + +| # | Test | Commit | +|---|------|--------| +| 1 | `test_table_consumed_block_ids_do_not_drop_same_id_reference_on_later_page` | P0 | +| 2 | `test_cross_page_table_asset_id_does_not_consume_same_id_on_caption_page` | P0 anti-regression | +| 3 | `test_table_caption_still_consumed` | P0 regression | +| 4 | `test_skip_section_grouping_places_tail_nonref_after_refs` | P1 | +| 5 | `test_skip_section_grouping_keeps_ordinary_nonref_before_refs` | P1 | +| 6 | `test_real_backmatter_heading_still_attaches_its_own_body` | P1 regression | +| 7 | `test_phase_4b_does_not_swallow_tail_nonref_into_ref_section` | P2 | +| 8 | `test_funding_body_still_attaches_to_funding_heading` | P2 regression | +| 9 | `test_page_continuation_marker_is_not_reference` | P3 | +| 10 | `test_real_reference_is_still_reference` | P3 regression | +| 11 | `test_refs_on_heading_page_are_rendered_after_heading` | P4 | +| 12 | `test_non_ref_blocks_not_moved_by_guard` | P4 regression | + +--- + +## Effort Estimate + +| Commit | Files | Lines Changed | Complexity | Risk | +|--------|-------|--------------|------------|------| +| 1 (P0) | `ocr_render.py` | ~20 add, ~10 remove | Medium | Table note consumption regression | +| 2 (P1) | `ocr_render.py` | ~15 add, ~5 remove | Low | backmatter_roles change is additive | +| 3 (P2) | `ocr_render.py` | ~10 add | Low | Guard after _find_owning_heading is safe | +| 4 (P3) | `ocr_families.py` | ~30 add, ~3 insert | Low | Regex + width gate, covered by tests | +| 5 (P4) | `ocr_render.py` | ~40 add, ~3 insert | Medium | Only moves refs, never deletes | + +**Total:** ~100-120 lines changed, 12 new tests, full regression on 9 papers. diff --git a/docs/superpowers/specs/2026-07-02-reference-detection-fix-spec.md b/docs/superpowers/specs/2026-07-02-reference-detection-fix-spec.md new file mode 100644 index 00000000..ef11d0b5 --- /dev/null +++ b/docs/superpowers/specs/2026-07-02-reference-detection-fix-spec.md @@ -0,0 +1,443 @@ +# OCR Reference Detection Fix — Specification v3 + +> **Status:** Spec complete — all root causes validated via trace evidence +> **Implementation-ready:** Tracks 1, 2a, 3, 5 +> **Limitation (no fix):** Track 4 — Wiley heading not in OCR text layer +> **Conditional:** Track 5b (4AG67PBH bio split) +> **Date:** 2026-07-02 + +--- + +## Track 1: `(N)` Parenthetical Reference Number Support + +**Files:** `ocr_roles.py`, `ocr_render.py`, `ocr_reference_signals.py` +**Status: EXECUTABLE** + +### Root Cause + +Three regex code paths check reference number prefix formats but none accept `(N)`: + +| Code path | File:Line | Accepts | Missing | +|-----------|-----------|---------|---------| +| `_REFERENCE_PATTERN` | `ocr_roles.py:72` | `N. ` / `et al.` / `(Name et al., YYYY)` | `(N) ` | +| `_ref_number_sort_key` | `ocr_render.py:488` | `N.` / `N)` / `[N]` | `(N)` | +| `has_number_lead` in `score_reference_entry()` | `ocr_reference_signals.py:37` | `[N]` / `N.` / `N)` / bare `N` | `(N)` | + +**Corpus impact:** 30/500 papers (6%) use `(N)` format. 9ZIJTI6J alone has 506 `(N)` blocks, of which 496 are misclassified as `backmatter_body`. + +### Changes + +#### 1a. `_REFERENCE_PATTERN` — `ocr_roles.py:72` + +Add `\(\d+\)\s` as the **first** alternative (to avoid collision with parenthetical author-year patterns): + +```python +_REFERENCE_PATTERN = re.compile( + r"^\s*(?:\(\d+\)\s|\d+\.\s|[A-Z][A-Za-z'’\-]+\s+et al\.\s*\(\d{4}[a-z]?\)|\([A-Z][A-Za-z'’\-]+\s+et al\.,\s*\d{4}[a-z]?\))", +) +``` + +**Length guard:** NOT inside `_REFERENCE_PATTERN` itself. Place in `assign_block_role()` around line 1361-1369 where `_looks_like_reference` is consumed: + +```python +_PAREN_REF_PREFIX = re.compile(r"^\s*\(\d+\)\s*") + +# text with reference-like pattern +if _looks_like_reference(text): + first_word = text.strip().split(",")[0].strip().lower() + if first_word not in _BODY_ORDINAL_OPENINGS: + # Length guard: (N) prefix with very short body → likely a heading, not a ref + stripped = _PAREN_REF_PREFIX.sub("", text).strip() + if text.lstrip().startswith("(") and len(stripped) < 25: + pass # skip — short (N) text is not a reference item + else: + return RoleAssignment( + role="reference_item", + confidence=0.6, + evidence=[f"reference-like pattern: {text[:60]}"], + ) +``` + +#### 1b. `_ref_number_sort_key` — `ocr_render.py:488` + +```python +m = re.match(r"^\s*(?:(\d+)[\.\)]|\[(\d+)\]|\((\d+)\))", text) +``` + +Return value captures third group: + +```python +if m: + num = m.group(1) or m.group(2) or m.group(3) + return (0, int(num)) +return (1, text) +``` + +#### 1c. `has_number_lead` — `ocr_reference_signals.py:37` + +**⚠️ IMPORTANT: do NOT use `\\d` in raw string — that matches literal `\d`, not digits.** + +Current broken spelling is conceptual only — actual code may be fine. Verify in source first. The correct regex: + +```python +has_number_lead = bool( + re.match(r"^\s*(\(\d+\)|\[\d+\]|\d+[\.)]?)(\s+|$)", text) +) +``` + +### Acceptance + +- Among blocks matching `(N)` prefix + author/volume/journal signals and inside detected reference/tail zone, ≥95% become `reference_item`. +- No body-zone short headings like "(1) Introduction" become `reference_item`. +- Sort order: `(1)` before `(2)` before `(3)` in emit. + +--- + +## Track 2a: Reference Heading Variant Expansion + +**Files:** `ocr_roles.py` (not `_detect_reference_zones`) +**Status: EXECUTABLE** — location identified, helper contract defined + +### Root Cause + +Role assignment fails to classify "References and Notes", "Bibliography", "Cited References" as `reference_heading`. These headings end up as `subsection_heading` or other roles, causing `reference_zone.status = HOLD` and blocking reference section assembly. + +**KUR9PBJC:** "References and Notes" classified as `subsection_heading` in `body_zone`. The fulltext shows `### References and Notes` at wrong heading level, and 4 refs are missing. + +### Changes + +**Do NOT modify `_detect_reference_zones()`.** That function consumes existing `reference_heading` roles; it doesn't assign them. + +Add a new helper and integrate into `assign_block_role()`: + +```python +_REFERENCE_HEADING_PATTERN = re.compile( + r"^(?:" + r"references?" + r"|references?\s+and\s+(?:notes?|further\s+reading)" + r"|bibliography" + r"|cited\s+references?" + r")$", + re.IGNORECASE, +) + +def _normalize_heading_text(text: str) -> str: + """Strip leader dots, trailing page numbers, and trailing colon. + + 'References ..... 42' → 'References' + 'References:' → 'References' + 'References and Notes ..... 3054' → 'References and Notes' + """ + text = text.strip().rstrip(":") + text = re.sub(r"\.{2,}\s*\d+\s*$", "", text) + text = re.sub(r"\s+\d+\s*$", "", text) + return text.strip() + + +def _is_reference_heading_text(text: str) -> bool: + """Check if text represents a reference section heading. + Uses fullmatch to prevent false positives like 'References in this article'. + """ + return bool(_REFERENCE_HEADING_PATTERN.fullmatch(_normalize_heading_text(text))) +``` + +Then in `assign_block_role()`, add a check for heading-like blocks (raw_label in `{"paragraph_title", "section_heading", "subsection_heading"}` or short text blocks near zone boundary) before they get assigned a final role: + +```python +# Check for reference heading text before heading role assignment +heading_text = text.strip() +if _is_reference_heading_text(heading_text): + return RoleAssignment( + role="reference_heading", + confidence=0.85, + evidence=[f"reference heading text match: {heading_text[:60]}"], + ) +``` + +Place this early enough in `assign_block_role()` that it runs before the generic heading → `section_heading` / `subsection_heading` assignment. The exact insertion point depends on the function structure — search for the point where `paragraph_title` raw_label is processed and add the reference_heading check before it. + +### Verification + +```python +@pytest.mark.parametrize("text", [ + "References", + "Reference", + "REFERENCES", + "References and Notes", + "References and Notes ..... 42", + "Bibliography", + "Cited References", +]) +def test_reference_heading_variants(text): + assert _is_reference_heading_text(text) + +@pytest.mark.parametrize("text", [ + "References in this article", + "Reference values", + "Further reading", + "References and results", +]) +def test_reference_heading_variants_rejects_non_headings(text): + assert not _is_reference_heading_text(text) +``` + +Paper rebuild: +```bash +python scripts/dev/ocr_rebuild_paper.py KUR9PBJC +# Check: "References and Notes" role is reference_heading +# Check: fulltext has proper ## References section +``` + +--- + +## Track 3: Cross-Page Reference Partition Consistency (WNDJX4KB) + +**Files:** `ocr_document.py` (`_normalize_reference_roles_from_partition`) +**Status: EXECUTABLE** — root cause confirmed via trace evidence + +### Root Cause + +Trace evidence from WNDJX4KB blocks 1-6 (page 8, heading page) vs 7-26 (page 9+): + +| Field | Blocks 1-6 (page 8) | Blocks 7-26 (page 9+) | +|-------|--------------------|----------------------| +| `raw_label` | `reference_content` | `reference_content` | +| `seed_role` | `reference_item` | `reference_item` | +| `style_family` | `reference_like` | `reference_like` | +| `zone` | `reference_zone` | `reference_zone` | +| **Final role** | **`body_paragraph`** | **`reference_item`** | + +ALL blocks have evidence `["reference content label: ..."]` — set by `assign_block_role()`. No evidence from `resolve_final_role()`, meaning it returned the same role. The demotion happens in **`_normalize_reference_roles_from_partition()`** which runs after role resolution. + +`_normalize_reference_roles_from_partition()` demotes `reference_item` blocks that are NOT in the reference partition. Page 8 blocks (same page as "References" heading) are excluded from the partition because the partition starts tracking from the page AFTER the heading page. + +### Fix Contract + +In `_normalize_reference_roles_from_partition()`, add a guard that preserves blocks the OCR explicitly identified as reference content, even when the automated partition boundary misses them: + +```python +# Before demoting a reference_item block outside the partition: +seed = str(block.get("seed_role") or "") +raw = str(block.get("raw_label") or block.get("block_label") or "") +block_zone = str(block.get("zone") or "") + +if (seed == "reference_item" and "reference" in block_zone) or \ + (raw == "reference_content" and "reference" in block_zone): + continue # skip demotion, keep as reference_item +``` + +This is safer than fixing the partition algorithm itself (which may have other edge cases). The guard only triggers when BOTH the OCR label and zone alignment agree it's a reference block. + +### Verification + +```bash +python scripts/dev/ocr_rebuild_paper.py WNDJX4KB +# Check: blocks 1-6 on page 8 have role=reference_item (not body_paragraph) +``` + +--- + +## Track 4: Wiley Heading Missing — OCR Limitation + +**Files:** None +**Status: LIMITATION** — no pipeline fix possible + +### Root Cause (Confirmed) + +Trace evidence from `97M7HFCD` and `2HEUD5P9`: +- `references_start` page has body subsections, publisher watermarks, running headers +- **NO block in the entire paper contains "References", "REFERENCES", or any variant** +- `reference_zone.status=HOLD`, `heading_block_id=None` +- Pipeline set `references_start` based on first `reference_item` block page (not heading) + +The "References" heading is not present in the PaddleOCR text output. It's either: +1. Embedded in a graphical element (PDF vector text skipped by OCR) +2. Merged with running header / noise at the header zone +3. Rendered in a font variant that PaddleOCR classifies as `header_image` + +**No pipeline fix:** The text simply isn't in the block layer. Synthetic heading is unsafe because `references_start` page still contains body content and the `reference_item` blocks on that page are fake (article tracking numbers like "2409400"). + +### Design Constraint + +If a future investigation determines the heading IS extractable, do NOT add synthetic heading generation unless ALL of: +- Dense `reference_item` block run exists in `reference_zone` +- Block run starts after body end (last `body_paragraph` y-position < first ref y-position) +- No competing `backmatter_heading` before the ref run + +--- + +## Track 5a: Reference Rendering Preservation (U746UJ7G — Already Fixed) + +**Files:** `ocr_render.py` (`_reorder_tail_run` emit path) +**Status: DIAGNOSTIC** — U746UJ7G no longer has the issue + +### Root Cause (Historical) + +Prior trace evidence showed refs 40, 41, 43 missing from fulltext in U746UJ7G. +**Rebuild after P0-P4 + layout robustness commits confirms all 46 refs are +present.** No numbering collision currently exists. The paper was fixed +by earlier pipeline improvements. + +### Fix Contract + +**Do NOT dedup by ref number.** Different refs sharing a number is an OCR +numbering error, not content duplication. Dropping by number loses valid refs. + +Add a **preservation invariant test** that verifies all `reference_item` blocks +in input appear in output, plus **collision logging** for diagnostics only. + +=== CRITICAL: Insertion Position === +The collision/logging code MUST be placed in `_reorder_tail_run()` between +`ref_section["bodies"].sort(key=_ref_number_sort_key)` and +`result.extend(ref_section["bodies"])`. If placed after extend, the +modifications have no effect on output. + +Collision logging code (after sort, before extend): + +```python +# Collision diagnostic: log duplicate ref numbers. +# Do NOT drop by number — different refs sharing a number is an OCR +# numbering error, not duplicate content. Dropping loses valid refs. +seen_numbers: set[int] = set() +for block in ref_section["bodies"]: + key = _ref_number_sort_key(block) + if key[0] == 0: + num = key[1] + if num in seen_numbers: + import logging + logging.warning( + f"Duplicate ref number {num}: " + f"'{str(block.get('text',''))[:60]}'" + ) + seen_numbers.add(num) +``` + +**No exact-text dedup either.** Commit 4 is diagnostic only. If exact-text +dedup is ever needed, it must be a separate future change with its own tests. + +### Verification + +```bash +pytest tests/test_ocr_render.py::test_reorder_tail_run_preserves_all_reference_items \ + tests/test_ocr_render.py::test_reorder_tail_run_preserves_duplicate_numbered_refs -v +python scripts/dev/ocr_rebuild_paper.py U746UJ7G +python -c "import re; t=open(r'D:/L/OB/Literature-hub/System/PaperForge/ocr/U746UJ7G/fulltext.md',encoding='utf-8').read(); print(all(re.search(rf'^{n}\. ',t,re.MULTILINE) for n in [40,41,42,43]))" +``` + +Expected: True (all refs already present before this change). + +## Track 5b: 4AG67PBH Bio Post-Reference Split (Conditional) + +**Status: CONDITIONAL** — re-test after Tracks 2a and 3 + +Track 2a (heading variants) and Track 3 (partition consistency) may fix this. But it is **NOT guaranteed** — even with a reference heading and correct partition, post-reference backmatter boundary still needs to know where refs end and bios begin. + +### Post-Track-2a+3 Re-test + +```bash +python scripts/dev/ocr_rebuild_paper.py 4AG67PBH +``` + +Check: +- Are bio blocks still in `reference_zone`? +- Is there a `backmatter_heading` or `backmatter_boundary_heading` separating bios from refs? + +If bios remain in `reference_zone`: add a post-reference backmatter split rule that triggers when `backmatter_body` blocks appear in `reference_zone` after a dense `reference_item` run. + +--- + +--- + +## Execution Plan + +### Commit 1: `(N)` reference support + +**Files:** `ocr_roles.py`, `ocr_render.py`, `ocr_reference_signals.py`, `ocr_document.py`, `tests/` + +1. `_REFERENCE_PATTERN`: add `\(\d+\)\s` alternative +2. `assign_block_role()`: add length guard for `(N)` short text +3. `_ref_number_sort_key`: add `\((\d+)\)` capture +4. `has_number_lead`: add `\(\d+\)` alternative (NOT `\\d+`) +5. `_check_reference_completeness()`: add `\(\d+\)` extraction at line 3237 +6. Add `assign_block_role("(1) Introduction") != reference_item` test + +### Commit 2: Reference heading variants + +**Files:** `ocr_roles.py`, `tests/` +**Rebase on:** Commit 1 (same file `ocr_roles.py`) + +1. Add `_is_reference_heading_text()` using `fullmatch()` (not `match()` + `\b`) +2. Add `rstrip(":")` in `_normalize_heading_text()` +3. Integrate into `assign_block_role()` before generic heading assignment +4. Tests: 7 valid variants + 4 false positives; remove unrelated `_PAREN_REF_PREFIX` import + +### Commit 3: Cross-page partition demotion guard + +**Files:** `ocr_document.py`, `tests/` +**Independent of:** Commits 1, 2 (different file) + +1. In `_normalize_reference_roles_from_partition()`, add guard: skip demotion if `seed_role == "reference_item"` + `"reference"` in zone +2. Test must construct a real "outside partition + reference_zone" case — no TODO/pass +3. WNDJX4KB rebuild verification + +### Commit 4: Reference rendering preservation + collision logging + +**Files:** `ocr_render.py`, `tests/` +**Depends on:** Commit 1 (`_ref_number_sort_key` update) + +1. Add preservation invariant test: ALL reference_item blocks in → out (including duplicates) +2. Add collision logging: log duplicate ref numbers, do NOT skip/drop them +3. Allow only exact-duplicate text dedup (same block text) +4. U746UJ7G rebuild verification — if still missing, trace deeper in render pipeline (not `_reorder_tail_run`) + +### Conditional: 4AG67PBH bio split (RE-TEST AFTER COMMITS 2+3) + +No code yet. Re-test after heading variants + partition fix. + +### No fix: Track 4 (Wiley heading) + +Heading text not in OCR output. Documented as limitation. + +--- +## Test Plan + +### Track 1 tests (Commit 1) + +| Test | File | What | +|------|------|------| +| `test_reference_pattern_matches_short_paren_heading_pattern_only` | `test_ocr_roles.py` | `_looks_like_reference` matches `(N)` pattern | +| `test_assign_block_role_rejects_short_paren_heading` | `test_ocr_roles.py` | `(1) Introduction` → NOT reference_item | +| `test_ref_number_sort_key_paren_format` | `test_ocr_render.py` | `(5)` → sort key (0,5) | +| `test_score_reference_entry_paren_format` | `test_ocr_document.py` | signal detects `(N)` as numbered | + +### Track 2a tests (Commit 2) + +| Test | File | What | +|------|------|------| +| `test_reference_heading_variants` (parametrized) | `test_ocr_roles.py` | 7 valid variants match | +| `test_reference_heading_variants_rejects_body_phrase` (parametrized) | `test_ocr_roles.py` | 4 false positives rejected | + +### Track 3 tests (Commit 3) + +| Test | File | What | +|------|------|------| +| `test_normalize_reference_roles_preserves_reference_content_in_zone` | `test_ocr_document.py` | seed_role=reference_item + ref zone → not demoted; _decision_log has partition_fallback | + +### Track 5a tests (Commit 4) + +| Test | File | What | +|------|------|------| +| `test_reorder_tail_run_preserves_duplicate_numbered_refs` | `test_ocr_render.py` | duplicate ref numbers with different text → both survive, collision logged | +| `test_reorder_tail_run_preserves_all_reference_items` | `test_ocr_render.py` | All ref items in → all ref items out | + +### Paper rebuild assertions (manual) + +| Paper | After commit | Assertion | +|-------|-------------|-----------| +| 9ZIJTI6J | Commit 1 | ≥95% `(N)` blocks = reference_item | +| KUR9PBJC | Commit 2 | "References and Notes" = reference_heading | +| WNDJX4KB | Commit 3 | blocks 1-6 on page 8 = reference_item | +| U746UJ7G | Commit 4 | refs 40, 41, 43 in fulltext | +| 4AG67PBH | Conditional | post-track-2+3: bios not in reference_zone | + +All existing tests must continue to pass after each commit. diff --git a/docs/superpowers/specs/2026-07-02-reference-zone-ordering-fix-spec.md b/docs/superpowers/specs/2026-07-02-reference-zone-ordering-fix-spec.md new file mode 100644 index 00000000..89d9eda5 --- /dev/null +++ b/docs/superpowers/specs/2026-07-02-reference-zone-ordering-fix-spec.md @@ -0,0 +1,360 @@ +# Reference Zone Fix — Specification v2 + +> **Status:** Spec complete — root causes validated, implementation contract hardened +> **Problem rate:** 14/50 papers (28%) have ref ordering/leakage anomalies +> **Approach:** 5 commits, each independently verifiable + +--- + +## Commit 1: P0 — Table Consumed Key Page Collision + +### Root Cause + +`ocr_render.py:1010-1015` builds a flat `block_page_by_id` dict keyed by per-page `block_id` (not globally unique). Last-write-wins overwrites earlier pages' entries. Then at line 1017-1022, `consumed_table_block_keys` uses this dict to resolve each table's `consumed_block_ids` to a page — resolving to the wrong page when the same `block_id` exists on a later page. The render loop at line 1438-1442 then silently skips ref blocks whose `(page, block_id)` matches the consumed key. + +### Fix Contract + +**Do NOT** simply swap to `table.get("page")`. Build consumed keys with **explicit per-block page** from table inventory fields, not from a flat dict. + +```python +def _add_consumed_key( + keys: set[tuple[int | None, str | int]], + page: int | None, + block_id: str | int, +) -> None: + """Add (page, block_id) and (page, str(block_id)) to consumed keys.""" + if block_id is None or block_id == "": + return + keys.add((page, block_id)) + keys.add((page, str(block_id))) +``` + +Then in the table loop: + +```python +consumed_table_block_keys: set[tuple[int | None, str | int]] = set() +for table in table_inventory.get("tables", []): + table_page = table.get("page") + + # Caption block — always on table's page + _add_consumed_key(consumed_table_block_keys, table_page, table.get("caption_block_id")) + + # Asset segments — each has its own page (caption ±1) + for seg in table.get("segments", []): + _add_consumed_key(consumed_table_block_keys, seg.get("page"), seg.get("asset_block_id")) + + # Note blocks on same page + for bid in table.get("note_block_ids", []): + _add_consumed_key(consumed_table_block_keys, table_page, bid) + + # Bridge/continuation blocks — same page as caption + for bid in table.get("bridge_block_ids", []): + _add_consumed_key(consumed_table_block_keys, table_page, bid) + + # Legacy fallback: consumed_block_ids table.page (no global lookup) + for bid in table.get("consumed_block_ids", []): + _add_consumed_key(consumed_table_block_keys, table_page, bid) +``` + +**Long-term contract:** `ocr_tables.py` should directly produce `consumed_block_keys: [{"page": ..., "block_id": ...}]`. Render should only consume this page-keyed output, never re-derive page from flat dict. + +### Verification + +``` +test_table_consumed_block_ids_do_not_drop_same_id_reference_on_later_page → P0 fix +test_table_caption_still_consumed → regression +``` + +**Papers to re-verify:** 37LK5T97 (refs 100-101), B43QSAJP (17-18), 62LTMCI8 (139-143), 4KCHGV2Z (3-5, 7-8), 58UFL9UN (120-121), JQMRCEXY (16-20) + +--- + +## Commit 2: P1 — `skip_section_grouping` Ordering + +### Root Cause + +When `skip_section_grouping=True` (pages with `reference_item` blocks but no `reference_heading`), the code emits `non_ref + refs + backmatter + fnotes`. This places `body_paragraph` blocks in `zone=tail_nonref_hold_zone` ("Address correspondence to:", "E-mail:", "Received/Accepted") before refs on the same page. + +### Fix Contract + +1. **`backmatter_roles`** must include `backmatter_boundary_heading`: + +```python +backmatter_roles = frozenset({ + "backmatter_body", + "backmatter_heading", + "backmatter_boundary_heading", +}) +``` + +2. **Ordering**: `ordinary_non_ref + refs + backmatter + tail_backmatter + fnotes` + +3. **Tail backmatter detection**: Use `zone=tail_nonref_hold_zone` as primary signal, pattern match as weak fallback: + +```python +_TAIL_BACKMATTER_CONTINUATION_PATTERN = re.compile( + r"^(?:address correspondence|correspondence|e-?mail|email|" + r"received|accepted|published|available online|" + r"author contributions?|conflicts? of interest|funding|" + r"acknowledg(?:e)?ments?)\b", + re.IGNORECASE, +) + +def _is_tail_backmatter_continuation(block: dict) -> bool: + zone = str(block.get("zone") or "") + if zone == "tail_nonref_hold_zone": + return True + text = str(block.get("text") or block.get("block_content") or "").strip() + return bool(_TAIL_BACKMATTER_CONTINUATION_PATTERN.match(text)) +``` + +4. **Modify skip branch:** + +```python +if skip_section_grouping: + ref_roles = frozenset({"reference_heading", "reference_item", "reference_body"}) + backmatter_roles = frozenset({...}) + + non_ref_all = [b for b in tail_blocks if b.get("role") not in ref_roles + and b.get("role") not in backmatter_roles and b.get("role") != "footnote"] + refs = sorted([b for b in tail_blocks if b.get("role") in ref_roles], key=_ref_number_sort_key) + backmatter = [b for b in tail_blocks if b.get("role") in backmatter_roles] + fnotes = [b for b in tail_blocks if b.get("role") == "footnote"] + + tail_backmatter = [b for b in non_ref_all if _is_tail_backmatter_continuation(b)] + ordinary_non_ref = [b for b in non_ref_all if not _is_tail_backmatter_continuation(b)] + + return (ordinary_non_ref + refs + backmatter + tail_backmatter + fnotes, + carried_ref, carried_backmatter) +``` + +### Verification + +``` +test_skip_section_grouping_places_tail_nonref_after_refs → positive test +test_skip_section_grouping_keeps_ordinary_nonref_before_refs → negative test +test_real_backmatter_heading_still_attaches_its_own_body → funding/ack not orphaned +``` + +--- + +## Commit 3: P2 — Phase 4b Tail Nonref Guard (non-skip path) + +### Root Cause + +In the non-skip path, `body_pool` blocks that fail `_find_owning_heading()` can fall through to `ref_section["bodies"]`. This is the same symptom as P1 but via a different code path. + +### Fix Contract + +Guard must be placed **after** `_find_owning_heading()` (not before it), so that real backmatter bodies (Funding, Acknowledgments) still attach to their own heading: + +```python +tail_backmatter_blocks: list[dict] = [] + +for body in body_pool: + idx = _find_owning_heading(body, backmatter_sections, page_width) + if idx is not None: + backmatter_sections[idx]["bodies"].append(body) + continue + + if _is_tail_backmatter_continuation(body): + tail_backmatter_blocks.append(body) # NOT orphan_blocks + continue + + # Original carried_backmatter / ref_section / orphan logic remains + ... +``` + +**Emit order** (Phase 5): + +```python +result.extend(sec_order_blocks) # backmatter sections +result.extend(ref_section_blocks) # references +result.extend(tail_backmatter_blocks) # ← inserted here, before footnotes +result.extend(footnote_blocks) +result.extend(orphan_blocks) +``` + +This ensures backmatter continuation appears after refs, not before them. + +### Verification + +``` +test_phase_4b_does_not_swallow_tail_nonref_into_ref_section → positive +test_funding_body_still_attaches_to_funding_heading → anti-regression +``` + +--- + +## Commit 4: P3 — Page Continuation Marker False Reference + +### Root Cause + +"X of Y" page markers (61px wide, e.g. "13 of 18", "13. of 18") match `reference_like` style family through three entry points with no exclusion gate. + +### Fix Contract + +Regex must cover variants seen in real data: `13 of 18`, `13. of 18`, `Page 13 of 18`, `13/18`: + +```python +_PAGE_CONTINUATION_MARKER_PATTERN = re.compile( + r"^(?:page\s*)?\d{1,4}\s*(?:[\.\-–—]?\s+of\s+|/)\s*\d{1,4}$", + re.IGNORECASE, +) +``` + +Helper with width gate: + +```python +def _looks_like_page_continuation_marker(block: dict) -> bool: + text = str(block.get("text") or block.get("block_content") or "").strip() + if not _PAGE_CONTINUATION_MARKER_PATTERN.match(text): + return False + + bbox = block.get("bbox") or block.get("block_bbox") or [] + width = float(bbox[2]) - float(bbox[0]) if len(bbox) >= 4 else None + layout_sig = block.get("layout_signature") or {} + if layout_sig.get("width") is not None: + width = float(layout_sig["width"]) + + if width is not None: + return width < 180 + return len(text.split()) <= 3 +``` + +Gate at three entry points in `ocr_families.py`: + +```python +# In _is_reference_family_candidate() +if _looks_like_page_continuation_marker(block): + return False + +# In _reference_anchor_matches_block() +if _looks_like_page_continuation_marker(block): + return False + +# In _has_reference_text_structure() +if _looks_like_page_continuation_marker(block): + return False +``` + +### Verification + +``` +test_page_continuation_marker_is_not_reference → "13 of 18", "13. of 18", "Page 13 of 18", "13/18" +test_real_reference_is_still_reference → "13. Smith J, Wang L. Cartilage repair in 2018." +``` + +**Papers to re-verify:** 62LTMCI8, TXMVULD7, JQMRCEXY — fake refs gone. + +--- + +## Commit 5: P4 — Same-Page Ref Blocks Before Reference Heading + +### Root Cause + +`_order_tail_blocks` (via `_sort_blocks_by_column`) can place some `reference_item` blocks ABOVE the `reference_heading` on the same page — but only for pages that pass the tail-page gate (`_body_count <= _tail_count`). Pages that fail the gate keep original reading order, which may also place refs before the heading if the PDF's internal order does so. + +### Fix Contract + +**Do NOT** only fix column-sort. Use a unified helper applied to **all page block lists** that have a `reference_heading`: + +```python +def _force_reference_heading_before_same_page_refs(page_blocks: list[dict]) -> list[dict]: + """Reorder page blocks so reference_item/reference_body always follow + the first reference_heading on the same page. Non-ref blocks are unchanged.""" + headings = [b for b in page_blocks if b.get("role") == "reference_heading"] + if not headings: + return page_blocks + + ref_roles = {"reference_item", "reference_body"} + refs = [b for b in page_blocks if b.get("role") in ref_roles] + if not refs: + return page_blocks + + first_heading = headings[0] + others = [b for b in page_blocks if b is not first_heading and b.get("role") not in ref_roles] + + # Insert all refs immediately after the heading + out: list[dict] = [] + inserted = False + for b in others: + out.append(b) + if b is first_heading: + inserted = True + out.extend(sorted(refs, key=_ref_number_sort_key)) + + if not inserted: + # Fallback: heading wasn't in `others` (unlikely), find original position + heading_idx = page_blocks.index(first_heading) + before = [b for b in page_blocks[:heading_idx] if b.get("role") not in ref_roles] + after = [b for b in page_blocks[heading_idx:] if b.get("role") not in ref_roles and b is not first_heading] + return before + [first_heading] + sorted(refs, key=_ref_number_sort_key) + after + + return out +``` + +Apply in `_order_tail_blocks` AFTER column-sort, before passing to `_reorder_tail_run`: + +```python +if page in tail_pages: + pw = page_widths.get(page, 1200) + sorted_blocks = _sort_blocks_by_column(page_blocks, pw) + sorted_blocks = _force_reference_heading_before_same_page_refs(sorted_blocks) + ordered, carried_ref, carried_backmatter = _reorder_tail_run( + sorted_blocks, ... + ) + result.extend(ordered) +``` + +### Verification + +``` +test_refs_on_heading_page_are_rendered_after_heading → positive +test_non_ref_blocks_not_moved_by_guard → negative +``` + +**Papers to re-verify:** 95FDVE4W (ref 2), WV2FF4NV (ref 9), 58UFL9UN (refs 9, 30, 31) + +--- + +## Regression Testing: Final Paper Checklist + +| Paper | Current State | Expected After All Fixes | +|-------|--------------|-------------------------| +| 37LK5T97 | missing 100, 101; backmatter intrudes | 118 refs in section, continuous; backmatter after refs | +| B43QSAJP | missing 17, 18 | 54 refs, continuous | +| 62LTMCI8 | missing 139-143; 6 fake "X of 18" | 152 refs, no fake refs | +| 4KCHGV2Z | missing 3-5, 7-8, 20-22 | 25 refs, continuous | +| 58UFL9UN | missing 9,30,31,115,116,120,121 | 132 refs, continuous | +| TXMVULD7 | missing 39; 5 fake "X of 16" | 73 refs, no fake refs | +| JQMRCEXY | missing 16-20; 2 fake refs | 21 refs, no fake refs | +| 95FDVE4W | ref 2 before heading | 24 refs in section | +| WV2FF4NV | ref 9 before heading | 77 refs in section | + +### Unit Tests + +``` +test_table_consumed_block_ids_do_not_drop_same_id_reference_on_later_page → P0 +test_table_caption_still_consumed → P0 regression +test_skip_section_grouping_places_tail_nonref_after_refs → P1 +test_skip_section_grouping_keeps_ordinary_nonref_before_refs → P1 +test_real_backmatter_heading_still_attaches_its_own_body → P1 regression +test_phase_4b_does_not_swallow_tail_nonref_into_ref_section → P2 +test_funding_body_still_attaches_to_funding_heading → P2 regression +test_page_continuation_marker_is_not_reference → P3 +test_real_reference_is_still_reference → P3 regression +test_refs_on_heading_page_are_rendered_after_heading → P4 +test_non_ref_blocks_not_moved_by_guard → P4 regression +``` + +## Appendix: Full Scan Results (50 papers) + +| Verdict | Count | Key | +|---------|-------|-----| +| ✅ Clean | 36 | Various | +| ⚠️ P0 (block_page_by_id) | 6 | 37LK5T97, B43QSAJP, 62LTMCI8, 4KCHGV2Z, 58UFL9UN, JQMRCEXY | +| ⚠️ P1 (skip_section_grouping) | 1 | 37LK5T97 | +| ⚠️ P3 (page marker) | 3 | 62LTMCI8, TXMVULD7, JQMRCEXY | +| ⚠️ P4 (ref before heading) | 3 | 95FDVE4W, WV2FF4NV, 58UFL9UN | +| Uses `[N]` format (audit false positive) | 5 | 53B47JM8, 49NUE2G7, 24A2QUAH, X6PQAH4V, PP76T2EY | diff --git a/paperforge/worker/ocr_document.py b/paperforge/worker/ocr_document.py index dcdb997b..56ead06e 100644 --- a/paperforge/worker/ocr_document.py +++ b/paperforge/worker/ocr_document.py @@ -3234,6 +3234,12 @@ def _check_reference_completeness(blocks: list[dict]) -> dict: for block in ref_items: text = (block.get("text") or "").strip() # Try bracket pattern: [1] + # Try parenthetical pattern: (1) + m = _re.match(r"^\s*\((\d+)\)", text) + if m: + numbers.append(int(m.group(1))) + continue + m = _re.match(r"^\s*\[(\d+)\]", text) if m: numbers.append(int(m.group(1))) @@ -5513,6 +5519,24 @@ def normalize_document_structure( tail_spread = _build_tail_boundary_from_ref_partition(partition, region_bus) ref_partition_active = tail_spread is not None + # Post-partition fallback: restore reference_item for blocks that OCR + # explicitly identified as reference content but were excluded from the + # reference partition boundary (WNDJX4KB pattern — heading-page refs). + for block in blocks: + zone = str(block.get("zone") or "") + seed = str(block.get("seed_role") or "") + raw = str(block.get("raw_label") or block.get("block_label") or "") + if block.get("role") == "body_paragraph" and "reference" in zone: + if seed == "reference_item" or raw == "reference_content": + block["role"] = "reference_item" + record_decision( + block, + stage="partition_fallback", + old_role="body_paragraph", + new_role="reference_item", + reason="reference_content block outside partition, restored from seed_role", + ) + if ref_partition_active: # Pre-ref blocks must NOT be in tail_nonref_hold_zone — they are body flow. # infer_zones() may have placed them there before the ref partition was diff --git a/paperforge/worker/ocr_reference_signals.py b/paperforge/worker/ocr_reference_signals.py index ed8dacca..29384415 100644 --- a/paperforge/worker/ocr_reference_signals.py +++ b/paperforge/worker/ocr_reference_signals.py @@ -34,7 +34,7 @@ def score_reference_entry(text: str) -> dict: has_vol_pages = bool(re.search(r"\b\d+\s*\(\d+\)\s*:\s*[A-Za-z0-9\-]+", text) or re.search(r"\b\d+\s*:\s*[A-Za-z0-9\-]+", text)) has_online = any(token in lower for token in ("[internet]", "available from", "doi:", "pmid:", "pmcid:", "published online", "cited ")) has_report_markers = any(token in lower for token in ("guideline", "organization", "committee", "available from")) or "[internet]" in lower - has_number_lead = bool(re.match(r"^\s*(\[\d+\]|\d+[\.)]?)(\s+|$)", text)) + has_number_lead = bool(re.match(r"^\s*(\(\d+\)|\[\d+\]|\d+[\.\)]?)(\s+|$)", text)) journal_match = _has_journal_match(text) family = "unknown" @@ -57,5 +57,6 @@ def score_reference_entry(text: str) -> dict: "volume_issue_pages_signature": has_vol_pages, "online_marker_signature": has_online, "journal_lexicon_match": journal_match, + "number_lead": has_number_lead, }, } diff --git a/paperforge/worker/ocr_render.py b/paperforge/worker/ocr_render.py index c19e610f..fbb10b84 100644 --- a/paperforge/worker/ocr_render.py +++ b/paperforge/worker/ocr_render.py @@ -481,13 +481,10 @@ def _attach_container_bodies( def _ref_number_sort_key(block: dict) -> tuple: text = str(block.get("text") or block.get("block_content") or "") - # Two capture groups — alternation prevents false matches on plain year numbers - # like "2024" that lack a period/bracket suffix. - # ponytail: only handles N. / N) / [N] prefix formats. Unnumbered refs fall - # through to lexicographic sort — upgrade to column-major sort if needed. - m = re.match(r"^\s*(?:(\d+)[\.\)]|\[(\d+)\])", text) + m = re.match(r"^\s*(?:(\d+)[\.\)]|\[(\d+)\]|\((\d+)\))", text) if m: - return (0, int(m.group(1) or m.group(2))) + num = m.group(1) or m.group(2) or m.group(3) + return (0, int(num)) return (1, text) _TAIL_BACKMATTER_CONTINUATION_PATTERN = re.compile( @@ -771,6 +768,18 @@ def _reorder_tail_run( result.append(ref_section["heading"]) if ref_section.get("bodies"): ref_section["bodies"].sort(key=_ref_number_sort_key) + # Collision diagnostic: log duplicate ref numbers. + # Do NOT drop by number — different refs sharing a number is an OCR + # numbering error, not duplicate content. Dropping loses valid refs. + seen_numbers: set[int] = set() + for block in ref_section["bodies"]: + key = _ref_number_sort_key(block) + if key[0] == 0: + num = key[1] + if num in seen_numbers: + import logging + logging.warning(f"Duplicate ref number {num}: '{str(block.get('text',''))[:60]}'") + seen_numbers.add(num) result.extend(ref_section["bodies"]) result.extend(tail_backmatter_blocks) result.extend(footnote_blocks) diff --git a/paperforge/worker/ocr_roles.py b/paperforge/worker/ocr_roles.py index 6f657aaa..48da59ea 100644 --- a/paperforge/worker/ocr_roles.py +++ b/paperforge/worker/ocr_roles.py @@ -70,9 +70,11 @@ FRONTMATTER_NOISE = { } _REFERENCE_PATTERN = re.compile( - r"^\s*(?:\d+\.\s|[A-Z][A-Za-z'’\-]+\s+et al\.\s*\(\d{4}[a-z]?\)|\([A-Z][A-Za-z'’\-]+\s+et al\.,\s*\d{4}[a-z]?\))", + r"^\s*(?:\(\d+\)\s|\d+\.\s|[A-Z][A-Za-z'’\-]+\s+et al\.\s*\(\d{4}[a-z]?\)|\([A-Z][A-Za-z'’\-]+\s+et al\.,\s*\d{4}[a-z]?\))", ) +_PAREN_REF_PREFIX = re.compile(r"^\s*\(\d+\)\s*") + _FRONTIERS_FIGURE_TITLE_PATTERN = re.compile( r"^FIGURE\s+\d+[A-Za-z]?\s*\|\s+.+", flags=re.IGNORECASE, @@ -100,6 +102,27 @@ _FIGURE_DESCRIPTION_OPENING_PATTERN = re.compile( flags=re.IGNORECASE, ) +_REFERENCE_HEADING_PATTERN = re.compile( + r"^(?:" + r"references?" + r"|references?\s+and\s+(?:notes?|further\s+reading)" + r"|bibliography" + r"|cited\s+references?" + r")$", + re.IGNORECASE, +) + + +def _normalize_heading_text(text: str) -> str: + text = text.strip().rstrip(":") + text = re.sub(r"\.{2,}\s*\d+\s*$", "", text) + text = re.sub(r"\s+\d+\s*$", "", text) + return text.strip() + + +def _is_reference_heading_text(text: str) -> bool: + return bool(_REFERENCE_HEADING_PATTERN.fullmatch(_normalize_heading_text(text))) + def _looks_like_figure_description_opening(text: str) -> bool: return bool(_FIGURE_DESCRIPTION_OPENING_PATTERN.match(text.strip())) @@ -1259,6 +1282,13 @@ def assign_block_role( confidence=0.5, evidence=[f"unnumbered paragraph_title on page 1 outside title zone: {text[:60]}"], ) + heading_text = text.strip() + if _is_reference_heading_text(heading_text): + return RoleAssignment( + role="reference_heading", + confidence=0.85, + evidence=[f"reference heading text match: {heading_text[:60]}"], + ) level = _infer_heading_level(text, block=block) return RoleAssignment( role=level, @@ -1362,11 +1392,16 @@ def assign_block_role( if _looks_like_reference(text): first_word = text.strip().split(",")[0].strip().lower() if first_word not in _BODY_ORDINAL_OPENINGS: - return RoleAssignment( - role="reference_item", - confidence=0.6, - evidence=[f"reference-like pattern: {text[:60]}"], - ) + # Length guard: (N) prefix with very short body → likely a heading, not a ref + stripped = _PAREN_REF_PREFIX.sub("", text).strip() + if text.lstrip().startswith("(") and len(stripped) < 25: + pass # skip — short (N) text is not a reference item + else: + return RoleAssignment( + role="reference_item", + confidence=0.6, + evidence=[f"reference-like pattern: {text[:60]}"], + ) # text -> body paragraph by default, but with lower confidence if raw_label == "text": diff --git a/scripts/dev/ocr_deep_dive_analysis.py b/scripts/dev/ocr_deep_dive_analysis.py new file mode 100644 index 00000000..0d3375fd --- /dev/null +++ b/scripts/dev/ocr_deep_dive_analysis.py @@ -0,0 +1,248 @@ +"""Deep-dive: analyze real OCR problems found by batch audit. + +Investigates: +1. unknown_structural blocks — what content are they? (text samples) +2. Reference number gaps — are refs missing from fulltext or just misnumbered? +3. Backmatter leak to reference zone — which blocks and why? +4. Extreme outlier papers (9ZIJTI6J, WS6T79MU) +""" + +from __future__ import annotations + +import json +import os +import re +import sys +from collections import Counter, defaultdict +from pathlib import Path + + +def _load_blocks_jsonl(path: Path) -> list[dict]: + blocks: list[dict] = [] + if not path.exists(): + return blocks + with open(path, encoding="utf-8") as f: + for line in f: + line = line.strip() + if line: + blocks.append(json.loads(line)) + return blocks + + +def _text(block: dict) -> str: + return str(block.get("text") or block.get("block_content") or "") + + +def _analyze_unknowns(ocr_root: Path, keys: list[str]) -> None: + """Sample text content of unknown_structural blocks by zone.""" + print("=" * 70) + print("ANALYSIS 1: unknown_structural blocks — content sampling") + print("=" * 70) + + by_zone: dict[str, list[tuple[str, str]]] = defaultdict(list) # zone -> [(key, text)] + + for key in keys: + paper_dir = ocr_root / key + blocks = _load_blocks_jsonl(paper_dir / "structure" / "blocks.structured.jsonl") + for b in blocks: + if b.get("role") == "unknown_structural": + zone = str(b.get("zone", "unzoned")) + txt = _text(b)[:150] + by_zone[zone].append((key, txt)) + + for zone, samples in sorted(by_zone.items(), key=lambda x: -len(x[1])): + print(f"\n## Zone: {zone} ({len(samples)} blocks)") + # Show unique text patterns + patterns = Counter() + for _, txt in samples: + # First 60 chars as pattern key + pattern = txt[:60].strip() + if pattern: + patterns[pattern] += 1 + print("Top text patterns:") + for pat, cnt in patterns.most_common(20): + print(f" [{cnt}x] {pat}") + # Show a few random full samples + print("Sample entries:") + for key, txt in samples[:5]: + print(f" [{key}] zone={zone} | {txt}"[:200]) + + +def _analyze_ref_gaps(ocr_root: Path, keys: list[str]) -> None: + """Analyze reference number gaps — check if refs are in blocks but not in fulltext.""" + print("\n" + "=" * 70) + print("ANALYSIS 2: Reference number gaps — block vs fulltext comparison") + print("=" * 70) + + for key in keys[:15]: # top 15 gap papers + paper_dir = ocr_root / key + blocks = _load_blocks_jsonl(paper_dir / "structure" / "blocks.structured.jsonl") + ft_path = paper_dir / "fulltext.md" + ft_text = ft_path.read_text(encoding="utf-8") if ft_path.exists() else "" + + # Extract ref numbers from blocks + block_refs: set[int] = set() + for b in blocks: + role = b.get("role", "") + if role in ("reference_item",): + txt = _text(b) + m = re.match(r"^\s*(\d+)", txt) + if m: + block_refs.add(int(m.group(1))) + + # Extract ref numbers from fulltext + ft_refs = set() + for m in re.finditer(r"^(\d+)\.\s", ft_text, re.MULTILINE): + ft_refs.add(int(m.group(1))) + + # Which numbers are in blocks but missing from fulltext? + in_blocks_not_ft = sorted(block_refs - ft_refs) + # Which numbers are in fulltext but not as explicit refs? + # (This checks the ref_item count vs fulltext count) + n_block = len(block_refs) + n_ft = len(ft_refs) + + if in_blocks_not_ft or n_block != n_ft: + print(f"\n{key}: {n_block} refs in blocks, {n_ft} refs in fulltext") + if in_blocks_not_ft: + print(f" Blocks not in fulltext: {in_blocks_not_ft[:20]}") + # Show block roles around the gap + max_ref = max(block_refs) if block_refs else 0 + gaps = sorted(set(range(1, max_ref + 1)) - block_refs) + if gaps: + print(f" Missing ref numbers (neither block nor ft): {gaps[:20]}") + # Are there body_paragraph blocks that look like refs? + for b in blocks: + txt = _text(b) + if b.get("role") == "body_paragraph" and re.match(r"^\d+\.\s", txt.strip()): + print(f" Possible unclassified ref in body_paragraph: {txt[:100]}") + + +def _analyze_backmatter_leak(ocr_root: Path, keys: list[str]) -> None: + """Analyze papers with backmatter/body blocks leaking into reference zone.""" + print("\n" + "=" * 70) + print("ANALYSIS 3: Backmatter/body leak to reference zone") + print("=" * 70) + + for key in keys: + paper_dir = ocr_root / key + blocks = _load_blocks_jsonl(paper_dir / "structure" / "blocks.structured.jsonl") + ft_path = paper_dir / "fulltext.md" + ft_text = ft_path.read_text(encoding="utf-8") if ft_path.exists() else "" + + leak_blocks = [] + for b in blocks: + zone = str(b.get("zone", "")) + role = b.get("role", "") + if "reference" in zone and role in ("backmatter_body", "body_paragraph"): + leak_blocks.append(b) + print(f" [{key}] zone={zone} role={role} | {_text(b)[:100]}") + + if leak_blocks: + print(f"\n{key}: {len(leak_blocks)} leak blocks") + # Check if fulltext shows these blocks + for b in leak_blocks: + txt = _text(b)[:60].strip() + if txt and txt not in ft_text: + print(f" NOT in fulltext: {txt}") + + +def _analyze_catastrophic(ocr_root: Path, keys: list[str]) -> None: + """Deep analysis of catastrophic failure papers.""" + print("\n" + "=" * 70) + print("ANALYSIS 4: Catastrophic failure papers") + print("=" * 70) + + for key in keys: + paper_dir = ocr_root / key + ds_path = paper_dir / "structure" / "document_structure.json" + ds = json.loads(ds_path.read_text(encoding="utf-8")) if ds_path.exists() else {} + blocks = _load_blocks_jsonl(paper_dir / "structure" / "blocks.structured.jsonl") + ft_path = paper_dir / "fulltext.md" + ft_text = ft_path.read_text(encoding="utf-8") if ft_path.exists() else "" + + print(f"\n## {key}") + print(f" Figures: {len(ds.get('figure_inventory', []))}") + print(f" Tables: {len(ds.get('table_inventory', []))}") + print(f" Total blocks: {len(blocks)}") + print(f" Fulltext length: {len(ft_text)} chars") + + # Role distribution + role_counts = Counter(b.get("role", "") for b in blocks) + print(f" Top roles: {role_counts.most_common(10)}") + + # Zone distribution + zone_counts = Counter(str(b.get("zone", "")) for b in blocks) + print(f" Top zones: {zone_counts.most_common(10)}") + + # Show blocks that are in body_zone but unknown + unknowns = [b for b in blocks if b.get("role") == "unknown_structural"] + if unknowns: + print(f" unknown_structural sample:") + for b in unknowns[:10]: + print(f" zone={b.get('zone')} text={_text(b)[:100]}") + + # Show fulltext first 500 chars + print(f" Fulltext first 500 chars:") + print(f" {ft_text[:500].replace(chr(10), chr(10)+' ')}") + + # Show last 500 chars + print(f" Fulltext last 500 chars:") + print(f" {ft_text[-500:].replace(chr(10), chr(10)+' ')}") + + +def main() -> int: + ocr_root = Path( + os.environ.get("PAPERFORGE_OCR_ROOT") or os.environ.get("PAPERFORGE_REAL_OCR_ROOT") + or "D:/L/OB/Literature-hub/System/PaperForge/ocr" + ) + + # Find the 200 most recent papers with data + all_dirs = sorted([d for d in ocr_root.iterdir() if d.is_dir() and not d.name.startswith(".")], + key=lambda d: -d.stat().st_mtime) + all_keys = [d.name for d in all_dirs if (d / "structure" / "blocks.structured.jsonl").exists()] + print(f"Total available papers: {len(all_keys)}") + sample_keys = all_keys[:200] + + # 1. unknown_structural deep-dive + _analyze_unknowns(ocr_root, sample_keys) + + # 2. Find papers with ref gaps for deep analysis + gap_papers = [] + for key in sample_keys[:200]: + paper_dir = ocr_root / key + ft_path = paper_dir / "fulltext.md" + if not ft_path.exists(): + continue + ft_text = ft_path.read_text(encoding="utf-8") + ref_nums = re.findall(r"^(\d+)\.\s", ft_text, re.MULTILINE) + if ref_nums: + nums = sorted(int(n) for n in ref_nums) + expected = list(range(1, nums[-1] + 1)) + if sorted(set(expected) - set(nums)): + gap_papers.append(key) + print(f"\nRef gap papers in top 200: {len(gap_papers)}") + _analyze_ref_gaps(ocr_root, gap_papers[:15]) + + # 3. Find papers with backmatter leak to ref zone + leak_papers = [] + for key in sample_keys: + paper_dir = ocr_root / key + blocks = _load_blocks_jsonl(paper_dir / "structure" / "blocks.structured.jsonl") + for b in blocks: + zone = str(b.get("zone", "")) + role = b.get("role", "") + if "reference" in zone and role in ("backmatter_body", "body_paragraph"): + leak_papers.append(key) + break + print(f"\nBackmatter leak to ref zone papers: {len(leak_papers)}") + _analyze_backmatter_leak(ocr_root, leak_papers) + + # 4. Catastrophic papers + _analyze_catastrophic(ocr_root, ["9ZIJTI6J", "WS6T79MU"]) + + return 0 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/scripts/dev/ocr_reference_zone_audit.py b/scripts/dev/ocr_reference_zone_audit.py new file mode 100644 index 00000000..787c737a --- /dev/null +++ b/scripts/dev/ocr_reference_zone_audit.py @@ -0,0 +1,389 @@ +"""Reference zone integrity + ordering + body continuity diagnostic. + +Checks across many processed papers: +1. Reference ordering: are reference numbers strictly increasing? +2. Zone leakage: are non-reference blocks between reference items? +3. Body continuity: does body text flow across pages without gaps? +4. Figure/table matching: basic count health. +""" + +from __future__ import annotations + +import argparse +import json +import re +import sys +from collections.abc import Iterable +from pathlib import Path +from typing import Any + + +def _find_repo_root(start: Path) -> Path: + current = start.resolve() + for parent in [current] + list(current.parents): + if (parent / ".git").exists(): + return parent + raise RuntimeError(f"No repo root from {start}") + + +_THIS_FILE = Path(__file__).resolve() +_REPO_ROOT = _find_repo_root(_THIS_FILE) +if str(_REPO_ROOT) not in sys.path: + sys.path.insert(0, str(_REPO_ROOT)) + +from paperforge.worker.ocr_artifacts import artifact_paths_for_root # noqa: E402 + +# Regex: standard ref number prefixes (1. / 1) / [1] / (1)) +_REF_NUM_RE = re.compile(r"^\s*(?:(\d+)[\.\)]|\[(\d+)\]|\((\d+)\))\s*") +# Detect body paragraph start (non-empty, non-reference, non-heading) +_BODY_START_RE = re.compile(r"^[A-Z][^.]+[.?!]") + + +def _load_json(path: Path, default: Any = None) -> Any: + if not path.exists(): + return default + try: + return json.loads(path.read_text(encoding="utf-8")) + except Exception: + return default + + +def _load_block_trace_csv(path: Path) -> list[dict[str, str]]: + import csv + if not path.exists(): + return [] + with open(path, encoding="utf-8") as fh: + return list(csv.DictReader(fh)) + + +def _resolve_ocr_root(raw: str | None) -> Path: + candidate = raw or os.environ.get("PAPERFORGE_OCR_ROOT") or os.environ.get("PAPERFORGE_REAL_OCR_ROOT") + # backstop: relative to repo + if not candidate: + candidate = str(_REPO_ROOT / ".." / ".." / "OB" / "Literature-hub" / "System" / "PaperForge" / "ocr") + path = Path(candidate) + if not path.exists(): + path = _REPO_ROOT.parent / "ocr" + return path.resolve() + + +def _find_paper_keys(ocr_root: Path, limit: int = 0) -> list[str]: + """Return paper keys sorted by mtime (newest first).""" + entries = sorted( + [d for d in ocr_root.iterdir() if d.is_dir() and not d.name.startswith("_") and not d.name.startswith(".")], + key=lambda d: d.stat().st_mtime, + reverse=True, + ) + keys = [d.name for d in entries] + return keys[:limit] if limit > 0 else keys + + +def _parse_ref_number(text: str) -> int | None: + """Extract reference number from standard prefix formats.""" + m = _REF_NUM_RE.match(text) + if m: + for g in m.groups(): + if g is not None: + return int(g) + return None + + +def _analyze_reference_ordering(fulltext: str) -> dict: + """Check reference ordering and non-reference intrusion. + + Scans from first `## References` (or `# References`) to end. + """ + ref_section_text = "" + for sep in ["\n## References\n", "\n# References\n", "\n## Bibliography\n"]: + if sep in fulltext: + ref_section_text = fulltext.split(sep, 1)[1] + break + + if not ref_section_text: + return {"status": "no_ref_section", "count": 0, "issues": []} + + issues: list[dict] = [] + blocks: list[dict] = [] + current_text = "" + current_num = None + + for line in ref_section_text.split("\n"): + line_stripped = line.strip() + if not line_stripped: + continue + num = _parse_ref_number(line_stripped) + if num is not None: + if current_text: + blocks.append({"number": current_num, "text": current_text[:80]}) + current_text = line_stripped + current_num = num + elif line_stripped.startswith("