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audit: vision audit of 2HEUD5P9 + 4AG67PBH (4 oracle agents)

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2HEUD5P9 (10 findings):
  - Frontmatter P1: 17/17 correct (PASS)
  - Figures P4/P6/P9/P10/P15/P21: all correct (PASS)
  - Figure on P13: caption mislabeled as body_paragraph (BUG)
  - Boundary P23: clean body/ref transition (PASS)

4AG67PBH (11 findings):
  - Frontmatter P1: 3 footnote->affiliation mismatches (BUG)
  - Frontmatter P1: 2 frontmatter_noise->support mismatches (MINOR)
  - Figures P3: non_body_insert->figure_caption_candidate (BUG)
  - Figures P10: panel D over-segmented (MINOR)
  - Figures P25: author-bio page backmatter mislabel (BUG)
  - Boundary P21: Conflict of Interest heading/body wrong (BUG)
  - Figures P4/10/13/14/15: correctly grouped (PASS)

Cross-paper patterns identified:
  1. footnote_vs_affiliation (4AG67PBH)
  2. figure_caption_mislabel_as_body (both papers)
  3. backmatter_page_mislabel (4AG67PBH)
  4. zone_leak_frontmatter_to_body (both papers)
  5. reference_boundary_body_mix (both papers)
  6. title_repeat_on_page_2 (2HEUD5P9)
This commit is contained in:
Research Assistant 2026-06-28 23:40:08 +08:00
parent a2bb91a42c
commit 172c3b2590
17 changed files with 2087 additions and 12 deletions
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186
audit/2026-06-28-data-audit-findings.json
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@ -17,7 +17,10 @@
},
{
"severity": "BUG",
"pages": ["1", "23"],
"pages": [
"1",
"23"
],
"block_role": "frontmatter_noise",
"zone": "body_zone",
"text": "ORCID + Received/Revised dates",
@ -27,7 +30,20 @@
},
{
"severity": "MINOR",
"pages": ["2", "3", "6", "8", "10", "12", "16", "19", "22", "23", "25", "26"],
"pages": [
"2",
"3",
"6",
"8",
"10",
"12",
"16",
"19",
"22",
"23",
"25",
"26"
],
"block_role": "unknown_structural",
"zone": "body_zone",
"text": "empty or whitespace",
@ -39,20 +55,63 @@
"severity": "BUG",
"page": 23,
"zone_mix": true,
"zones": ["body_zone(7)", "reference_zone(45)", "frontmatter_side_zone(1)"],
"zones": [
"body_zone(7)",
"reference_zone(45)",
"frontmatter_side_zone(1)"
],
"issue": "body blocks intermixed with reference zone on page 23 — body blocks before reference boundary",
"expected": "body blocks should be pre-reference and reference_zone should start cleanly",
"category": "reference_boundary_body_leak"
},
{
"severity": "INFO",
"pages": ["1"],
"pages": [
"1"
],
"note": "Frontmatter clean: paper_title (2 blocks), authors (1 block) in frontmatter_main_zone"
},
{
"severity": "INFO",
"pages": ["1"],
"pages": [
"1"
],
"note": "Abstract: 1 abstract_body in body_zone — correct"
},
{
"severity": "PASS",
"domain": "frontmatter",
"note": "17/17 blocks correct on page 1",
"category": "visual_audit"
},
{
"severity": "BUG",
"domain": "figures",
"page": 13,
"block": "p13:6",
"issue": "Figure 4 caption mislabeled as body_paragraph (should be figure_caption)",
"category": "figure_caption_mislabel"
},
{
"severity": "PASS",
"domain": "boundary",
"page": 23,
"note": "Clean body/ref transition. No body-ref mixing found.",
"category": "visual_audit"
},
{
"severity": "PASS",
"domain": "figures",
"pages": [
4,
6,
9,
10,
15,
21
],
"note": "All figures correctly grouped, captions correct, panels covered.",
"category": "visual_audit"
}
]
},
@ -84,20 +143,93 @@
"severity": "BUG",
"page": 21,
"zone_mix": true,
"zones": ["body_zone(8)", "reference_zone(35)", "frontmatter_side_zone(1)"],
"zones": [
"body_zone(8)",
"reference_zone(35)",
"frontmatter_side_zone(1)"
],
"issue": "Mixed body + reference zone on page 21 with Conflict of Interest in frontmatter_side_zone",
"expected": "conflict of interest should be in tail zone or body_zone",
"category": "reference_boundary_mix"
},
{
"severity": "INFO",
"pages": ["1"],
"pages": [
"1"
],
"note": "Frontmatter clean: paper_title (1), authors (1) in frontmatter_main_zone"
},
{
"severity": "INFO",
"pages": ["1"],
"pages": [
"1"
],
"note": "Abstract: 1 abstract_body in body_zone — correct"
},
{
"severity": "BUG",
"domain": "frontmatter",
"page": 1,
"blocks": [
"p1:11",
"p1:13",
"p1:15"
],
"issue": "Affiliation blocks misclassified as footnote (3 blocks)",
"category": "footnote_vs_affiliation"
},
{
"severity": "MINOR",
"domain": "frontmatter",
"page": 1,
"blocks": [
"p1:12",
"p1:16"
],
"issue": "DOI/copyright: frontmatter_noise -> frontmatter_support",
"category": "noise_vs_support"
},
{
"severity": "BUG",
"domain": "figures",
"page": 3,
"blocks": [
"3:4",
"3:7",
"3:10"
],
"issue": "non_body_insert vs figure_caption_candidate mislabel",
"category": "figure_caption_mislabel"
},
{
"severity": "MINOR",
"domain": "figures",
"page": 10,
"issue": "Panel D split across 2 asset blocks",
"category": "figure_over_segmentation"
},
{
"severity": "BUG",
"domain": "figures",
"page": 25,
"blocks": [
"25:4",
"25:8",
"25:10"
],
"issue": "Author-bio page: caption/ref_item -> backmatter_body",
"category": "backmatter_mislabel"
},
{
"severity": "BUG",
"domain": "boundary",
"page": 21,
"blocks": [
"21:8",
"21:9"
],
"issue": "Conflict Interest heading/body mislabeled",
"category": "backmatter_heading_mislabel"
}
]
}
@ -105,21 +237,51 @@
"cross_paper_patterns": {
"zone_leak_frontmatter_to_body": {
"count": 2,
"papers": ["2HEUD5P9", "4AG67PBH"],
"papers": [
"2HEUD5P9",
"4AG67PBH"
],
"description": "ORCID/copyright/DOI/date metadata blocks in body_zone — likely from frontmatter normalization missing these specific text patterns",
"fix": "Add ORCID, DOI, and date text patterns to frontmatter_noise normalization in _normalize_frontmatter_blocks"
},
"reference_boundary_body_mix": {
"count": 2,
"papers": ["2HEUD5P9", "4AG67PBH"],
"papers": [
"2HEUD5P9",
"4AG67PBH"
],
"description": "Body paragraphs intermixed with reference zone on reference boundary pages",
"fix": "P1 backmatter boundary redesign should handle this — verify ref-anchored partition"
},
"title_repeat_on_page_2": {
"count": 1,
"papers": ["2HEUD5P9"],
"papers": [
"2HEUD5P9"
],
"description": "Section heading on page 2 classified as paper_title",
"fix": "Tighten doc_title raw_label check for page 2: only accept if text matches page 1 title"
},
"footnote_vs_affiliation": {
"count": 1,
"papers": [
"4AG67PBH"
],
"fix": "Add address-specific patterns to footnote detection."
},
"figure_caption_mislabel_as_body": {
"count": 2,
"papers": [
"2HEUD5P9",
"4AG67PBH"
],
"fix": "Relax caption rules for blocks below figure assets in display zones."
},
"backmatter_page_mislabel": {
"count": 1,
"papers": [
"4AG67PBH"
],
"fix": "Add backmatter page guard: pages after reference boundary should not create new figure objects."
}
}
}
}

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audit/2HEUD5P9/block_review_boundary.jsonl Normal file
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@ -0,0 +1,12 @@
{"block_id":"p23:3","page":23,"review_status":"reviewed","truth_role":"body_paragraph","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This is regular concluding body text in the upper-left column, clearly above the reference list area."}
{"block_id":"p23:4","page":23,"review_status":"reviewed","truth_role":"body_paragraph","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This paragraph continues the article discussion in the upper-left column and remains outside the reference list."}
{"block_id":"p23:5","page":23,"review_status":"reviewed","truth_role":"sub_subsection_heading","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"'Acknowledgements' is an endmatter heading in the left column before the reference entries start."}
{"block_id":"p23:6","page":23,"review_status":"reviewed","truth_role":"body_paragraph","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This acknowledgement funding text belongs to the pre-reference body/endmatter zone rather than the reference list."}
{"block_id":"p23:7","page":23,"review_status":"reviewed","truth_role":"subsection_heading","truth_zone":"frontmatter_side_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"'Conflict of Interest' is a short endmatter heading in the left column and is separate from the reference zone."}
{"block_id":"p23:8","page":23,"review_status":"reviewed","truth_role":"frontmatter_noise","truth_zone":"frontmatter_side_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"The single sentence declaring no conflict is ancillary article metadata/endmatter beside the body-to-reference transition, not a reference entry."}
{"block_id":"p23:9","page":23,"review_status":"reviewed","truth_role":"sub_subsection_heading","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"'Keywords' is another endmatter heading above the start of the references in the lower-left column."}
{"block_id":"p23:10","page":23,"review_status":"reviewed","truth_role":"body_paragraph","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This keyword line is non-reference article metadata and remains above the first numbered reference item."}
{"block_id":"p23:11","page":23,"review_status":"reviewed","truth_role":"frontmatter_noise","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"The received/revised/published dates are article metadata placed just above the reference list boundary, not reference content."}
{"block_id":"p23:12","page":23,"review_status":"reviewed","truth_role":"reference_item","truth_zone":"reference_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This is the first visible numbered citation in the lower-left column, marking the start of the reference zone on page 23."}
{"block_id":"p23:23","page":23,"review_status":"reviewed","truth_role":"reference_item","truth_zone":"reference_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This numbered citation at the top of the right column is a standard reference entry and confirms the right column is fully in the reference zone."}
{"block_id":"p23:55","page":23,"review_status":"reviewed","truth_role":"reference_item","truth_zone":"reference_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This bottom-right numbered citation remains part of the continuous reference list, showing the reference zone extends to the page end without body-text intrusion."}

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audit/2HEUD5P9/block_review_figures.jsonl Normal file
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@ -0,0 +1,12 @@
{"block_id":"p4:25","page":4,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_004.png","method":"visual"},"short_reason":"This is the true caption for Figure 2; it sits directly below one composite multi-panel figure spanning panels A-I, and the surrounding figure-asset boxes cover the visible panels on the page."}
{"block_id":"p4:18","page":4,"review_status":"reviewed","truth_role":"figure_label","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_004.png","method":"visual"},"short_reason":"The tiny '(I)' text above the bottom-right image group is only a panel label for subpanel I, not a standalone figure caption or separate figure."}
{"block_id":"p6:3","page":6,"review_status":"reviewed","truth_role":"table_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_006.png","method":"visual"},"short_reason":"This page contains Table 1 only; the displayed text is a table title above tabular rows and there is no figure on the page."}
{"block_id":"p9:26","page":9,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_009.png","method":"visual"},"short_reason":"This is the correct caption for the single composite Figure 3. The page shows one grouped figure with panels A-K, and the asset boxes cover those visible sub-panels without introducing a second caption."}
{"block_id":"p10:2","page":10,"review_status":"reviewed","truth_role":"table_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_010.png","method":"visual"},"short_reason":"This is the caption for Table 2 above a large table; page 10 is not a figure page and contains no figure caption or figure assets."}
{"block_id":"p13:6","page":13,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_013.png","method":"visual"},"short_reason":"This block is the true caption for Figure 4. It appears immediately above the Figure 4 panels A-E and describes the images beneath it, so it is not body paragraph text."}
{"block_id":"p13:13","page":13,"review_status":"reviewed","truth_role":"figure_label","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_013.png","method":"visual"},"short_reason":"The small '4 W' text is an in-panel timepoint label inside Figure 5E, not a figure caption or heading."}
{"block_id":"p13:15","page":13,"review_status":"reviewed","truth_role":"figure_label","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_013.png","method":"visual"},"short_reason":"The small '8 W' text is another in-panel timepoint label inside Figure 5E, not a caption or section heading."}
{"block_id":"p13:39","page":13,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_013.png","method":"visual"},"short_reason":"This is the correct caption for the lower composite Figure 5. The page visually contains one grouped figure with panels A-L, and the asset boxes cover the visible panels while the true caption sits directly below them."}
{"block_id":"p13:26","page":13,"review_status":"reviewed","truth_role":"figure_label","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_013.png","method":"visual"},"short_reason":"The tiny '(I)' marker above the lower-right image stack is just the panel label for Figure 5I, not a real figure caption."}
{"block_id":"p15:25","page":15,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_015.png","method":"visual"},"short_reason":"This is the correct caption for composite Figure 6. The caption text matches the visible panels A-G below it, and the colored asset boxes cover the sub-panels on the page rather than a heading or body block."}
{"block_id":"p21:17","page":21,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_021.png","method":"visual"},"short_reason":"This is the correct caption for composite Figure 8. It sits directly under panels A-F, and the figure-asset boxes cover the visible schematic, micro-CT, charts, and pathway panels of the same figure."}

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@ -0,0 +1,17 @@
{"block_id":"0","page":1,"review_status":"reviewed","truth_role":"frontmatter_noise","truth_zone":"frontmatter_main_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"The REVIEW badge is a page-top article-type label, not body content."}
{"block_id":"1","page":1,"review_status":"reviewed","truth_role":"frontmatter_noise","truth_zone":"frontmatter_main_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"This tiny top-edge box is page furniture near the header area, not semantic article text."}
{"block_id":"2","page":1,"review_status":"reviewed","truth_role":"frontmatter_noise","truth_zone":"frontmatter_main_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"The journal logo and website at the top-right are journal/header noise."}
{"block_id":"3","page":1,"review_status":"reviewed","truth_role":"paper_title","truth_zone":"frontmatter_main_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"This is the largest prominent text block near the top and is clearly the article title."}
{"block_id":"4","page":1,"review_status":"reviewed","truth_role":"authors","truth_zone":"frontmatter_main_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"This line is a sequence of author names directly beneath the title."}
{"block_id":"5","page":1,"review_status":"reviewed","truth_role":"abstract_body","truth_zone":"frontmatter_main_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"This dense introductory summary paragraph is the left-column portion of the abstract on page 1."}
{"block_id":"6","page":1,"review_status":"reviewed","truth_role":"section_heading","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"The numbered heading '1. Introduction' marks the start of the main body section."}
{"block_id":"7","page":1,"review_status":"reviewed","truth_role":"body_paragraph","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"This paragraph begins the introduction directly under the section heading."}
{"block_id":"8","page":1,"review_status":"reviewed","truth_role":"abstract_body","truth_zone":"frontmatter_main_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"This right-column text continues the abstract above the Introduction heading, so it is abstract text rather than a non-body insert."}
{"block_id":"9","page":1,"review_status":"reviewed","truth_role":"frontmatter_support","truth_zone":"frontmatter_main_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"This block contains author affiliations, emails, and correspondence details, which are frontmatter support metadata."}
{"block_id":"10","page":1,"review_status":"reviewed","truth_role":"body_paragraph","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"This is regular introduction body text in the right column below the section start."}
{"block_id":"11","page":1,"review_status":"reviewed","truth_role":"body_paragraph","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"This is another continuation paragraph of the introduction body text."}
{"block_id":"12","page":1,"review_status":"reviewed","truth_role":"frontmatter_support","truth_zone":"frontmatter_main_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"The ORCID note is article metadata/support text, not body content or journal furniture."}
{"block_id":"13","page":1,"review_status":"reviewed","truth_role":"frontmatter_support","truth_zone":"frontmatter_main_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"The DOI line is frontmatter support metadata for the article."}
{"block_id":"14","page":1,"review_status":"reviewed","truth_role":"frontmatter_noise","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"The journal citation line in the footer is page furniture/noise rather than article content."}
{"block_id":"15","page":1,"review_status":"reviewed","truth_role":"frontmatter_noise","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"The page/article number footer is pagination furniture, not semantic content."}
{"block_id":"16","page":1,"review_status":"reviewed","truth_role":"frontmatter_noise","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_001.png","method":"visual"},"short_reason":"The copyright footer at the bottom-right is publisher noise/page furniture."}

4
audit/2HEUD5P9/body_map.json Normal file
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@ -0,0 +1,4 @@
{
"paper": "2HEUD5P9",
"flagged_pages": []
}

439
audit/2HEUD5P9/figure_map.json Normal file
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@ -0,0 +1,439 @@
{
"paper": "2HEUD5P9",
"multi_asset_pages": [
{
"page": 4,
"asset_count": 14,
"caption_count": 2,
"risk_reasons": [
"multi_asset_page",
"caption_asset_mismatch",
"reader_object_gap"
],
"assets": [
{
"id": "3",
"bbox": "[121.0, 203.0, 311.0, 374.0]"
},
{
"id": "6",
"bbox": "[333.0, 204.0, 421.0, 375.0]"
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{
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"bbox": "[421.0, 200.0, 656.0, 398.0]"
},
{
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"bbox": "[657.0, 179.0, 848.0, 414.0]"
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{
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"bbox": "[887.0, 186.0, 969.0, 296.0]"
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{
"id": "12",
"bbox": "[973.0, 184.0, 1061.0, 296.0]"
},
{
"id": "13",
"bbox": "[886.0, 303.0, 967.0, 411.0]"
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{
"id": "14",
"bbox": "[967.0, 303.0, 1058.0, 412.0]"
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{
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{
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{
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},
{
"id": "22",
"bbox": "[424.0, 801.0, 694.0, 1167.0]"
}
],
"captions": [
{
"id": "18",
"text": "(1)"
},
{
"id": "25",
"text": "Figure 2. A) In vivo bone regeneration efficacy of whitlockite (WH: Ca $ _{18} $"
}
]
},
{
"page": 9,
"asset_count": 15,
"caption_count": 1,
"risk_reasons": [
"multi_asset_page",
"caption_asset_mismatch",
"reader_object_gap"
],
"assets": [
{
"id": "3",
"bbox": "[149.0, 158.0, 346.0, 306.0]"
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{
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{
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{
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"bbox": "[483.0, 601.0, 838.0, 766.0]"
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{
"id": "16",
"bbox": "[824.0, 601.0, 1085.0, 775.0]"
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"text": "advanced techniques, bioactive materials, bone regeneration, molecular mechanism"
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"text": "Received: September 22, 2023 \nRevised: November 4, 2023 \nPublished online: Mar"
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"text": "[40] V. Mouriño, R. Vidotto, J. P. Cattalini, A. R. Boccaccini, Curr. Opin. Biom"
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{
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