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pmid:40951359

Claudin18.2 defines a prognostically distinct subgroup of intrahepatic cholangiocarcinoma via CD8+ T-cell exclusion.

Frontiers in oncology · 2025 doi:10.3389/fonc.2025.1636367

Paper

partial

Experiment

partial

Data

partial

Analysis

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Execution

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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title
Claudin18.2 defines a prognostically distinct subgroup of intrahepatic cholangiocarcinoma via CD8+ T-cell exclusion.
doi
10.3389/fonc.2025.1636367
pmid
40951359
authors
null
journal
Frontiers in oncology
year
2025
abstract
null
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24.1
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quote
CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.
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the headline numerical result the paper states for its main finding
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Clinicopathological characteristics and CLDN18.2 expression in ICC patients.
structure object · 5 fields
pmcid
PMC12425741
section_index
8
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Clinicopathological features of ICC patients
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51
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6
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Table 1
caption
Clinicopathological characteristics and CLDN18.2 expression in ICC patients.
rows array · 51 items
[0] array · 5 items
[0]
Characteristics
[1]
Total (N=83)
[2]
Claudin18.2 expression
[3]
χ2
[4]
P value
[1] array · 2 items
[0]
Positive
[1]
Negative
[2] array · 6 items
[0]
Age (years)
[1]
[2]
[3]
[4]
0.019
[5]
0.89
[3] array · 6 items
[0]
≤ 65
[1]
55 (66.3%)
[2]
13 (65.0%)
[3]
42 (66.7%)
[4]
[5]
[4] array · 6 items
[0]
>65
[1]
28 (33.7%)
[2]
7 (35.0%)
[3]
21 (33.3%)
[4]
[5]
[5] array · 6 items
[0]
Sex
[1]
[2]
[3]
[4]
2.29
[5]
0.13
[6] array · 6 items
[0]
Female
[1]
26 (31.3%)
[2]
9 (45.0%)
[3]
17 (27.0%)
[4]
[5]
[7] array · 6 items
[0]
Male
[1]
57 (68.7%)
[2]
11 (55.0%)
[3]
46 (73.0%)
[4]
[5]
[8] array · 6 items
[0]
Tumor size (cm)
[1]
[2]
[3]
[4]
4.59
[5]
0.032*
[9] array · 6 items
[0]
≤ 5
[1]
45 (54.2%)
[2]
15 (75.0%)
[3]
30 (47.6%)
[4]
[5]
[10] array · 6 items
[0]
>5
[1]
38 (45.8%)
[2]
5 (25.0%)
[3]
33 (52.8%)
[4]
[5]
[11] array · 6 items
[0]
Tumor number
[1]
[2]
[3]
[4]
[5]
0.032*
[12] array · 6 items
[0]
1
[1]
70 (83.1%)
[2]
20 (100.0%)
[3]
50 (79.4%)
[4]
[5]
[13] array · 6 items
[0]
≥2
[1]
13 (16.9%)
[2]
0 (0.0%)
[3]
13 (20.6%)
[4]
[5]
[14] array · 6 items
[0]
Histological grade
[1]
[2]
[3]
[4]
H = 0.25
[5]
0.62
[15] array · 6 items
[0]
Well/Moderate
[1]
64 (77.1%)
[2]
16 (80.0%)
[3]
48 (76.2%)
[4]
[5]
[16] array · 6 items
[0]
Moderate-poor
[1]
9 (10.8%)
[2]
3 (15.0%)
[3]
6 (9.5%)
[4]
[5]
[17] array · 6 items
[0]
Poor
[1]
10 (12.0%)
[2]
1 (5.0%)
[3]
9 (14.3%)
[4]
[5]
[18] array · 6 items
[0]
Lymph node metastasis
[1]
[2]
[3]
[4]
[5]
0.35
[19] array · 6 items
[0]
Yes
[1]
18 (21.7%)
[2]
6 (30.0%)
[3]
12 (19.0%)
[4]
[5]
[20] array · 6 items
[0]
No
[1]
65 (78.3%)
[2]
14 (70.0%)
[3]
51 (81.0%)
[4]
[5]
[21] array · 6 items
[0]
AJCC TNM stage
[1]
[2]
[3]
[4]
1.07
[5]
0.30
[22] array · 6 items
[0]
I/II
[1]
65 (78.3%)
[2]
14 (70.0%)
[3]
51 (81.0%)
[4]
[5]
[23] array · 6 items
[0]
III/IV
[1]
18 (21.7%)
[2]
6 (30.0%)
[3]
12 (19.0%)
[4]
[5]
[24] array · 6 items
[0]
MVI
[1]
[2]
[3]
[4]
1.60
[5]
0.21
[25] array · 6 items
[0]
M0
[1]
48 (57.8%)
[2]
14 (70.0%)
[3]
34 (54.0%)
[4]
[5]
[26] array · 6 items
[0]
M1/M2
[1]
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[2]
6 (30.0%)
[3]
29 (46.0%)
[4]
[5]
[27] array · 6 items
[0]
aCA199
[1]
[2]
[3]
[4]
6.04
[5]
0.026*
[28] array · 6 items
[0]
Positive
[1]
48 (58.2%)
[2]
15 (83.3%)
[3]
33 (54.1%)
[4]
[5]
[29] array · 6 items
[0]
Negative
[1]
31 (41.8%)
[2]
3 (16.7%)
[3]
28 (45.9%)
[4]
[5]
[30] array · 6 items
[0]
HBV
[1]
[2]
[3]
[4]
2.97
[5]
0.085
[31] array · 6 items
[0]
Positive
[1]
47 (56.6%)
[2]
8 (40.0%)
[3]
39 (61.9%)
[4]
[5]
[32] array · 6 items
[0]
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[1]
36 (43.3%)
[2]
12 (60.0%)
[3]
24 (38.1%)
[4]
[5]
[33] array · 6 items
[0]
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[1]
[2]
[3]
[4]
0.17
[5]
0.68
[34] array · 6 items
[0]
Yes
[1]
30 (36.1%)
[2]
8 (40.0%)
[3]
22 (34.9%)
[4]
[5]
[35] array · 6 items
[0]
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[1]
53 (63.9%)
[2]
12 (60.0%)
[3]
41 (65.1%)
[4]
[5]
[36] array · 6 items
[0]
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[1]
[2]
[3]
[4]
0.07
[5]
0.78
[37] array · 6 items
[0]
Yes
[1]
27 (32.5%)
[2]
7 (35.0%)
[3]
20 (31.7%)
[4]
[5]
[38] array · 6 items
[0]
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[1]
56 (67.5%)
[2]
13 (65.0%)
[3]
43 (68.3%)
[4]
[5]
[39] array · 6 items
[0]
Cirrhosis
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[2]
[3]
[4]
[5]
0.43
[40] array · 6 items
[0]
Yes
[1]
10 (12.0%)
[2]
1 (5.0%)
[3]
9 (14.3%)
[4]
[5]
[41] array · 6 items
[0]
No
[1]
73 (88.0%)
[2]
19 (95.0%)
[3]
54 (85.7%)
[4]
[5]
[42] array · 6 items
[0]
aCEA
[1]
[2]
[3]
[4]
0.96
[5]
0.76
[43] array · 6 items
[0]
Positive
[1]
24 (30.4%)
[2]
6 (33.3%)
[3]
18 (29.5%)
[4]
[5]
[44] array · 6 items
[0]
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[1]
55 (69.6%)
[2]
12 (66.7%)
[3]
43 (70.5%)
[4]
[5]
[45] array · 6 items
[0]
a AFP
[1]
[2]
[3]
[4]
[5]
0.66
[46] array · 6 items
[0]
Positive
[1]
7 (8.9%)
[2]
2 (11.1%)
[3]
5 (8.2%)
[4]
[5]
[47] array · 6 items
[0]
Negative
[1]
72 (91.1%)
[2]
16 (88.9%)
[3]
56 (91.8%)
[4]
[5]
[48] array · 6 items
[0]
Recurrence
[1]
[2]
[3]
[4]
[5]
0.018*
[49] array · 6 items
[0]
Yes
[1]
57 (68.7%)
[2]
18 (90.0%)
[3]
39 (61.9%)
[4]
[5]
[50] array · 6 items
[0]
No
[1]
26 (31.3%)
[2]
2 (10.0%)
[3]
24 (38.1%)
[4]
[5]
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Univariate analysis of prognostic factors(OS) for ICC.
structure object · 5 fields
pmcid
PMC12425741
section_index
11
section_title
Prognostic significance of CLDN18.2 in ICC
row_count
18
column_count
4
table object · 8 fields
label
Table 2
caption
Univariate analysis of prognostic factors(OS) for ICC.
rows array · 18 items
[0] array · 4 items
[0]
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[1]
HR
[2]
95% CI
[3]
P value
[1] array · 4 items
[0]
Age (years) (> 65 vs. ≤ 65)
[1]
0.690
[2]
0.369-1.291
[3]
0.246
[2] array · 4 items
[0]
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[1]
0.805
[2]
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[3]
0.472
[3] array · 4 items
[0]
HBV
[1]
1.079
[2]
0.609-1.915
[3]
0.794
[4] array · 4 items
[0]
CA199
[1]
3.487
[2]
1.710-7.110
[3]
0.001*
[5] array · 4 items
[0]
CEA
[1]
1.638
[2]
0.885-3.032
[3]
0.116
[6] array · 4 items
[0]
TNM stage (III/IV vs. I/II)
[1]
2.165
[2]
1.129-4.151
[3]
0.020*
[7] array · 4 items
[0]
Histological grade
[1]
[2]
[3]
0.010*
[8] array · 4 items
[0]
(Moderate-poor vs. poor)
[1]
0.376
[2]
0.124-1.138
[3]
0.083
[9] array · 4 items
[0]
(Well-Moderate vs. poor)
[1]
0.312
[2]
0.147-0.660
[3]
0.002*
[10] array · 4 items
[0]
MVI (M1/M2 vs. M0)
[1]
2.600
[2]
1.459-4.635
[3]
0.001*
[11] array · 4 items
[0]
Lymph node metastasis
[1]
2.165
[2]
1.129-4.151
[3]
0.020*
[12] array · 4 items
[0]
Bile duct invasion
[1]
1.372
[2]
0.766-2.458
[3]
0.288
[13] array · 4 items
[0]
Perineural invasion
[1]
1.542
[2]
0.858-2.773
[3]
0.148
[14] array · 4 items
[0]
Tumor number (≥ 2 vs. 1)
[1]
0.885
[2]
0.396-1.977
[3]
0.766
[15] array · 4 items
[0]
Tumor size(cm) (> 5 vs. ≤ 5)
[1]
1.594
[2]
0.904-2.811
[3]
0.107
[16] array · 4 items
[0]
Cirrhosis
[1]
0.739
[2]
0.292-1.868
[3]
0.522
[17] array · 4 items
[0]
Claudin18.2
[1]
2.545
[2]
1.383-4.682
[3]
0.003*
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18
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Cox regression analyses of disease-free survival for ICC.
structure object · 5 fields
pmcid
PMC12425741
section_index
11
section_title
Prognostic significance of CLDN18.2 in ICC
row_count
11
column_count
5
table object · 8 fields
label
Table 3
caption
Cox regression analyses of disease-free survival for ICC.
rows array · 11 items
[0] array · 3 items
[0]
[1]
Univariable analysis
[2]
Multivariable analysis
[1] array · 5 items
[0]
Parameters
[1]
HR (95% CI)
[2]
P value
[3]
HR (95% CI)
[4]
P value
[2] array · 5 items
[0]
CA199
[1]
2.350 (1.311-4.213)
[2]
0.004*
[3]
1.517 (0.789-2.920)
[4]
0.212
[3] array · 5 items
[0]
TNM stage (III/IV vs. I/II)
[1]
2.594 (1.419-4.742)
[2]
0.002*
[3]
2.612 (1.313-5.197)
[4]
0.006*
[4] array · 5 items
[0]
Histological grade
[1]
[2]
0.049*
[3]
[4]
0.409
[5] array · 5 items
[0]
(Moderate-poor vs. poor)
[1]
0.637 (0.237-1.716)
[2]
0.373
[3]
0.606 (0.199-1.844)
[4]
0.378
[6] array · 5 items
[0]
(Well-Moderate vs. poor)
[1]
0.414 (0.199-0.860)
[2]
0.018*
[3]
0.549 (0.228-1.323)
[4]
0.181
[7] array · 5 items
[0]
MVI (M1/M2 vs. M0)
[1]
2.358 (1.384-4.019)
[2]
0.002*
[3]
2.086 (1.157-3.761)
[4]
0.014*
[8] array · 5 items
[0]
Lymph node metastasis
[1]
2.594 (1.419-4.742)
[2]
0.002*
[3]
2.612 (1.313-5.197)
[4]
0.006*
[9] array · 5 items
[0]
Claudin18.2
[1]
1.865 (1.053-3.304)
[2]
0.033*
[3]
2.229 (1.125-4.415)
[4]
0.022*
[10] array · 5 items
[0]
Tumor size (cm)(> 5 vs. ≤ 5)
[1]
1.832 (1.087-3.087)
[2]
0.023*
[3]
2.443 (1.357-4.400)
[4]
0.003*
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11
column_count
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39
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source_hash
dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63
raw_response_sha256
sha256:cbb5aedcdc7c06c9d206d8b65a11029776642d8c3620ee0f079eaea72308dc39
raw_response_chars
5984
[1] object · 7 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
full-text-reading-v1
prompt_hash
c81b3b92a26c17b1ceae580cb44e96f55b1ada2f7e644c1048fc94c99a37ee44
source_hash
dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63
raw_response_sha256
sha256:41fcda48ce2069e44282c23664441b539095a2203098363e259bb8b87f588cfd
raw_response_chars
63518
target_providers array · 2 items
[0] object · 8 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
replication-target-v2
prompt_hash
cdddd4a80760e7ead5577e92fb1cb6854de83a6a1040d2f9a3fcc5c9a7c48e3c
source_hash
dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63
raw_response
{"parent_value":24.1,"unit":"%","evidence":"CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.","target_result":"CLDN18.2 expression in 24.1% of intrahepatic cholangiocarcinoma tissues.","number_stated":true}
reading object · 6 fields
parent_value
24.1
unit
%
evidence
CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.
target_result
CLDN18.2 expression in 24.1% of intrahepatic cholangiocarcinoma tissues.
number_stated
true
source_locator
chars 890-986 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63
recorded_at
2026-10-31T15:36:01.124635+00:00
[1] object · 8 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
replication-target-v2
prompt_hash
8aad65e79d0263eb42a9b8816ad5b720de49f1d2f267dd6107d71ce38e1cc77f
source_hash
dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63
raw_response
<think>We need answer JSON object only. Need interpret target "headline numerical result paper states for its main finding" likely 24.1% expression? Need identify single numerical result replication registered target. Paper title/main finding CLDN18.2 defines subgroup via CD8 exclusion. Headline numerical result perhaps CLDN18.2 exclusively expressed in 24.1% (20/83) of ICC tissues. The wording conclusion: "this study establishes CLDN18.2 as a tumor-specific biomarker in ICC, expressed in 24.1% of ICC patients with absent normal tissue expression." They ask headline number only, value paper itself states, unit paper prints. Evidence exact contiguous quote contains number, if linked by wording quote whole clause. Need choose number and unit. parent_value number 24.1, unit "%" likely. Evidence exact contiguous quotation: "CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues." This is exact sentence, contains attribution and main result. target_result perhaps concise "24.1%" or "CLDN18.2 was exclusively expressed in 24.1% of ICC tissues." Since headline number only maybe parent_value 24.1, unit "%". target_result could "24.1%" or descriptive. Need not include converted count. Evidence whole clause due linked directly. Need ensure quote exact contiguous source. Yes. Could registered target instead be HR 2.555 for reduced OS, the headline numerical result for main finding? Need reason. They explicitly define target as "the headline numerical result the paper states for its main finding." In source, first result and conclusion emphasize expression prevalence 24.1%. Main title finding includes prognostic subgroup and CD8 exclusion, but no single exact headline beyond 24.1%. The instruction likely asks extraction benchmark where target generic, identify main numerical result. Usually abstracts have one headline number. Here likely 24.1% because conclusion repeats it. Need perhaps evidence quote whole conclusion clause: "In conclusion, this study establishes CLDN18.2 as a tumor-specific biomarker in ICC, expressed in 24.1% of ICC patients with absent normal tissue expression." This explicitly labels main finding. Better than result sentence. They demand "When that is how text links them, quote whole clause so reader can check attribution." We can quote entire exact sentence. Does evidence need only clause containing number? Exact contiguous. Use conclusion sentence. Unit printed "%" embedded. parent_value 24.1. target_result perhaps "24.1% of ICC patients" (headline number only asks report headline number only, perhaps target_result should just "24.1%"). JSON schema target_result string. We can say "24.1%" to comply headline number only, while evidence quote. They ask "Report the headline number only: the value..." So target_result likely "24.1%". Other fields required. Let's formulate. Need valid JSON no markdown. Ensure Unicode okay. Evidence exact: "In conclusion, this study establishes CLDN18.2 as a tumor-specific biomarker in ICC, expressed in 24.1% of ICC patients with absent normal tissue expression." Yes source exact. Could unit "%" and parent_value 24.1. number_stated true. Let's answer.</think> {"parent_value":24.1,"unit":"%","evidence":"In conclusion, this study establishes CLDN18.2 as a tumor-specific biomarker in ICC, expressed in 24.1% of ICC patients with absent normal tissue expression.","target_result":"24.1%","number_stated":true}
reading object · 6 fields
parent_value
24.1
unit
%
evidence
In conclusion, this study establishes CLDN18.2 as a tumor-specific biomarker in ICC, expressed in 24.1% of ICC patients with absent normal tissue expression.
target_result
24.1%
number_stated
true
source_locator
chars 5176-5333 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63
recorded_at
2026-10-31T15:36:06.297212+00:00
agreement
false
disagreements object · 4 fields
target_result object · 3 fields
minimax
CLDN18.2 expression was an independent prognostic factor for reduced overall survival (OS: HR = 2.555, 95% CI = 1.250–5.223, P = 0.01).
minimax_alt
Multivariable analysis identified CLDN18.2 as an independent prognostic factor for reduced overall survival (OS: HR = 2.555, 95% CI = 1.250–5.223, P = 0.01) and disease-free survival (DFS: HR = 2.229, 95% CI = 1.125–4.415, P = 0.022).
decisive
false
physical_methods object · 3 fields
minimax array · 2 items
[0]
Tissue microarray immunohistochemistry (IHC)
[1]
CD8+ tumor-infiltrating lymphocyte (TIL) quantification
minimax_alt array · 2 items
[0]
Immunohistochemistry (IHC) on tissue microarray sections from 83 ICC and 47 matched non-tumor tissues
[1]
CD8+ tumor-infiltrating lymphocyte (TIL) quantification
decisive
false
analysis_methods object · 3 fields
minimax array · 5 items
[0]
Single-sample gene set enrichment analysis (ssGSEA)
[1]
TIMER method in the IOBR R package
[2]
Kaplan-Meier method
[3]
Log-rank test
[4]
Cox proportional hazards regression
minimax_alt array · 10 items
[0]
Single-sample gene set enrichment analysis (ssGSEA)
[1]
TIMER method in the IOBR R package
[2]
Wilcoxon rank-sum test
[3]
chi-square test
[4]
Fisher's exact test
[5]
one-sample t-test
[6]
one-way ANOVA
[7]
Kaplan-Meier method
[8]
log-rank test
[9]
univariate and multivariate Cox proportional hazards regression
decisive
false
statistical_method object · 3 fields
minimax
Cox proportional hazards regression
minimax_alt
Multivariable Cox proportional hazards regression
decisive
true
agreement_basis object · 2 fields
policy
decisive_fields
decisive_fields array · 4 items
[0]
work_type
[1]
number_stated
[2]
parent_value
[3]
unit
blinded
true
human_critique object · 5 fields
status
not_run
reviewer
null
signed_at
null
conflict_checked
false
commentary
null
stages array · 7 items
[0] object · 4 fields
key
target_materials
status
pending
reason
null
evidence
null
[1] object · 4 fields
key
independent_readings
status
blocked
reason
The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 0 items
[2] object · 4 fields
key
source_resolution
status
pending
reason
null
evidence
null
[3] object · 4 fields
key
protocol_reconstruction
status
pending
reason
null
evidence
null
[4] object · 4 fields
key
control_execution
status
pending
reason
null
evidence
null
[5] object · 4 fields
key
control_comparison
status
pending
reason
null
evidence
null
[6] object · 4 fields
key
publication
status
pending
reason
null
evidence
null
gaps array · 2 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 1 item
[0] object · 3 fields
id
package:91c5e09e7a2593656663c98008024767d70a37641cfa6f2fcea7a8dc302a67fd
type
sep_package
label
SEP v1 package for pmid:40951359
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40951359
type
conversion
used array · 1 item
[0]
package:91c5e09e7a2593656663c98008024767d70a37641cfa6f2fcea7a8dc302a67fd
agent
agent:corpus-assay-engine
agents array · 3 items
[0] object · 3 fields
id
agent:minimax
type
model
label
minimax
[1] object · 3 fields
id
agent:minimax_alt
type
model
label
minimax_alt
[2] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
source_run_id
run-20261023T122449232913
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:40951359
parent_hash
sha256:bd7d6a92ad049c3211250ad193d8dc223da4165687ec8a7670c0474b8acd8c8e
fork_of
null
generation
2
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:40951359 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
method
[7]
review.human_critique
[8]
review.machine_critique.blocked
[9]
step:obtain_source_data blocked on data:not_downloaded
[10]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[11]
step:run_analysis input 'materials:the source data behind the published result in pmid:40951359' does not resolve to a declared asset
[12]
targets
Complete file 
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40951359", "kind": "science-record", "revision": 2, "content_hash": "sha256:253486a70cb3fa8e7f70d7dba9652e49061645eb758f3dd18d190d1bd5b8391c", "created_at": "2026-11-01T10:25:53Z", "updated_at": "2026-11-01T14:01:48Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Claudin18.2 defines a prognostically distinct subgroup of intrahepatic cholangiocarcinoma via CD8+ T-cell exclusion.", "doi": "10.3389/fonc.2025.1636367", "pmid": "40951359", "authors": null, "journal": "Frontiers in oncology", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 24.1, "unit": "percent", "tolerance": null, "source": "chars 890-986 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63"}, "evidence": [{"asset": "source:pmid:40951359", "locator": "chars 890-986 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63", "quote": "CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues."}]}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40951359"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:40951359", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40951359' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40951359", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2025.1636367", "sha256": "sha256:dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2025.1636367", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40951359:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1aab42c1c72036f14bcc3225dfaaaa0f1733eae2b4607332fed0d3eb77230452", "bytes": 2730, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#T1", "version": null, "note": "Clinicopathological characteristics and CLDN18.2 expression in ICC patients.", "structure": {"pmcid": "PMC12425741", "section_index": 8, "section_title": "Clinicopathological features of ICC patients", "row_count": 51, "column_count": 6}, "table": {"label": "Table 1", "caption": "Clinicopathological characteristics and CLDN18.2 expression in ICC patients.", "rows": [["Characteristics", "Total (N=83)", "Claudin18.2 expression", "χ2", "P value"], ["Positive", "Negative"], ["Age (years)", "", "", "", "0.019", "0.89"], ["≤ 65", "55 (66.3%)", "13 (65.0%)", "42 (66.7%)", "", ""], [">65", "28 (33.7%)", "7 (35.0%)", "21 (33.3%)", "", ""], ["Sex", "", "", "", "2.29", "0.13"], ["Female", "26 (31.3%)", "9 (45.0%)", "17 (27.0%)", "", ""], ["Male", "57 (68.7%)", "11 (55.0%)", "46 (73.0%)", "", ""], ["Tumor size (cm)", "", "", "", "4.59", "0.032*"], ["≤ 5", "45 (54.2%)", "15 (75.0%)", "30 (47.6%)", "", ""], [">5", "38 (45.8%)", "5 (25.0%)", "33 (52.8%)", "", ""], ["Tumor number", "", "", "", "", "0.032*"], ["1", "70 (83.1%)", "20 (100.0%)", "50 (79.4%)", "", ""], ["≥2", "13 (16.9%)", "0 (0.0%)", "13 (20.6%)", "", ""], ["Histological grade", "", "", "", "H = 0.25", "0.62"], ["Well/Moderate", "64 (77.1%)", "16 (80.0%)", "48 (76.2%)", "", ""], ["Moderate-poor", "9 (10.8%)", "3 (15.0%)", "6 (9.5%)", "", ""], ["Poor", "10 (12.0%)", "1 (5.0%)", "9 (14.3%)", "", ""], ["Lymph node metastasis", "", "", "", "", "0.35"], ["Yes", "18 (21.7%)", "6 (30.0%)", "12 (19.0%)", "", ""], ["No", "65 (78.3%)", "14 (70.0%)", "51 (81.0%)", "", ""], ["AJCC TNM stage", "", "", "", "1.07", "0.30"], ["I/II", "65 (78.3%)", "14 (70.0%)", "51 (81.0%)", "", ""], ["III/IV", "18 (21.7%)", "6 (30.0%)", "12 (19.0%)", "", ""], ["MVI", "", "", "", "1.60", "0.21"], ["M0", "48 (57.8%)", "14 (70.0%)", "34 (54.0%)", "", ""], ["M1/M2", "35 (42.2%)", "6 (30.0%)", "29 (46.0%)", "", ""], ["aCA199", "", "", "", "6.04", "0.026*"], ["Positive", "48 (58.2%)", "15 (83.3%)", "33 (54.1%)", "", ""], ["Negative", "31 (41.8%)", "3 (16.7%)", "28 (45.9%)", "", ""], ["HBV", "", "", "", "2.97", "0.085"], ["Positive", "47 (56.6%)", "8 (40.0%)", "39 (61.9%)", "", ""], ["Negative", "36 (43.3%)", "12 (60.0%)", "24 (38.1%)", "", ""], ["Microbiliary invasion", "", "", "", "0.17", "0.68"], ["Yes", "30 (36.1%)", "8 (40.0%)", "22 (34.9%)", "", ""], ["No", "53 (63.9%)", "12 (60.0%)", "41 (65.1%)", "", ""], ["Perineural invasion", "", "", "", "0.07", "0.78"], ["Yes", "27 (32.5%)", "7 (35.0%)", "20 (31.7%)", "", ""], ["No", "56 (67.5%)", "13 (65.0%)", "43 (68.3%)", "", ""], ["Cirrhosis", "", "", "", "", "0.43"], ["Yes", "10 (12.0%)", "1 (5.0%)", "9 (14.3%)", "", ""], ["No", "73 (88.0%)", "19 (95.0%)", "54 (85.7%)", "", ""], ["aCEA", "", "", "", "0.96", "0.76"], ["Positive", "24 (30.4%)", "6 (33.3%)", "18 (29.5%)", "", ""], ["Negative", "55 (69.6%)", "12 (66.7%)", "43 (70.5%)", "", ""], ["a AFP", "", "", "", "", "0.66"], ["Positive", "7 (8.9%)", "2 (11.1%)", "5 (8.2%)", "", ""], ["Negative", "72 (91.1%)", "16 (88.9%)", "56 (91.8%)", "", ""], ["Recurrence", "", "", "", "", "0.018*"], ["Yes", "57 (68.7%)", "18 (90.0%)", "39 (61.9%)", "", ""], ["No", "26 (31.3%)", "2 (10.0%)", "24 (38.1%)", "", ""]], "row_count": 51, "column_count": 6, "numeric_cells": 136, "header_rows": 2, "locator": "section[8]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:40951359:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b5eb6e48f3679d227f8cf8f4736118d3f4e82b2c446866cf4e8156e23f7e7685", "bytes": 1134, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T2", "version": null, "note": "Univariate analysis of prognostic factors(OS) for ICC.", "structure": {"pmcid": "PMC12425741", "section_index": 11, "section_title": "Prognostic significance of CLDN18.2 in ICC", "row_count": 18, "column_count": 4}, "table": {"label": "Table 2", "caption": "Univariate analysis of prognostic factors(OS) for ICC.", "rows": [["Parameters", "HR", "95% CI", "P value"], ["Age (years) (> 65 vs. ≤ 65)", "0.690", "0.369-1.291", "0.246"], ["Sex (male vs. female)", "0.805", "0.445-1.455", "0.472"], ["HBV", "1.079", "0.609-1.915", "0.794"], ["CA199", "3.487", "1.710-7.110", "0.001*"], ["CEA", "1.638", "0.885-3.032", "0.116"], ["TNM stage (III/IV vs. I/II)", "2.165", "1.129-4.151", "0.020*"], ["Histological grade", "", "", "0.010*"], ["(Moderate-poor vs. poor)", "0.376", "0.124-1.138", "0.083"], ["(Well-Moderate vs. poor)", "0.312", "0.147-0.660", "0.002*"], ["MVI (M1/M2 vs. M0)", "2.600", "1.459-4.635", "0.001*"], ["Lymph node metastasis", "2.165", "1.129-4.151", "0.020*"], ["Bile duct invasion", "1.372", "0.766-2.458", "0.288"], ["Perineural invasion", "1.542", "0.858-2.773", "0.148"], ["Tumor number (≥ 2 vs. 1)", "0.885", "0.396-1.977", "0.766"], ["Tumor size(cm) (> 5 vs. ≤ 5)", "1.594", "0.904-2.811", "0.107"], ["Cirrhosis", "0.739", "0.292-1.868", "0.522"], ["Claudin18.2", "2.545", "1.383-4.682", "0.003*"]], "row_count": 18, "column_count": 4, "numeric_cells": 55, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:40951359:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2a90d93ef13d5c831142a70f6defc9210d5d16a69362d23681f247dadf7a6830", "bytes": 1060, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#T3", "version": null, "note": "Cox regression analyses of disease-free survival for ICC.", "structure": {"pmcid": "PMC12425741", "section_index": 11, "section_title": "Prognostic significance of CLDN18.2 in ICC", "row_count": 11, "column_count": 5}, "table": {"label": "Table 3", "caption": "Cox regression analyses of disease-free survival for ICC.", "rows": [["", "Univariable analysis", "Multivariable analysis"], ["Parameters", "HR (95% CI)", "P value", "HR (95% CI)", "P value"], ["CA199", "2.350 (1.311-4.213)", "0.004*", "1.517 (0.789-2.920)", "0.212"], ["TNM stage (III/IV vs. I/II)", "2.594 (1.419-4.742)", "0.002*", "2.612 (1.313-5.197)", "0.006*"], ["Histological grade", "", "0.049*", "", "0.409"], ["(Moderate-poor vs. poor)", "0.637 (0.237-1.716)", "0.373", "0.606 (0.199-1.844)", "0.378"], ["(Well-Moderate vs. poor)", "0.414 (0.199-0.860)", "0.018*", "0.549 (0.228-1.323)", "0.181"], ["MVI (M1/M2 vs. M0)", "2.358 (1.384-4.019)", "0.002*", "2.086 (1.157-3.761)", "0.014*"], ["Lymph node metastasis", "2.594 (1.419-4.742)", "0.002*", "2.612 (1.313-5.197)", "0.006*"], ["Claudin18.2", "1.865 (1.053-3.304)", "0.033*", "2.229 (1.125-4.415)", "0.022*"], ["Tumor size (cm)(> 5 vs. ≤ 5)", "1.832 (1.087-3.087)", "0.023*", "2.443 (1.357-4.400)", "0.003*"]], "row_count": 11, "column_count": 5, "numeric_cells": 39, "header_rows": 2, "locator": "section[11]/table-wrap[2]#T3"}}], "gaps": ["asset:source:pmid:40951359 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40951359", "asset:table:pmid:40951359:1", "asset:table:pmid:40951359:2", "asset:table:pmid:40951359:3"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40951359"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "16b66414b037ad691896559f070f892472d0e188eead0adfd5147723f1499e86", "source_hash": "dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63", "raw_response_sha256": "sha256:cbb5aedcdc7c06c9d206d8b65a11029776642d8c3620ee0f079eaea72308dc39", "raw_response_chars": 5984}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "c81b3b92a26c17b1ceae580cb44e96f55b1ada2f7e644c1048fc94c99a37ee44", "source_hash": "dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63", "raw_response_sha256": "sha256:41fcda48ce2069e44282c23664441b539095a2203098363e259bb8b87f588cfd", "raw_response_chars": 63518}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "cdddd4a80760e7ead5577e92fb1cb6854de83a6a1040d2f9a3fcc5c9a7c48e3c", "source_hash": "dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63", "raw_response": "{\"parent_value\":24.1,\"unit\":\"%\",\"evidence\":\"CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.\",\"target_result\":\"CLDN18.2 expression in 24.1% of intrahepatic cholangiocarcinoma tissues.\",\"number_stated\":true}", "reading": {"parent_value": 24.1, "unit": "%", "evidence": "CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.", "target_result": "CLDN18.2 expression in 24.1% of intrahepatic cholangiocarcinoma tissues.", "number_stated": true, "source_locator": "chars 890-986 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63"}, "recorded_at": "2026-10-31T15:36:01.124635+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "8aad65e79d0263eb42a9b8816ad5b720de49f1d2f267dd6107d71ce38e1cc77f", "source_hash": "dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63", "raw_response": "<think>We need answer JSON object only. Need interpret target \"headline numerical result paper states for its main finding\" likely 24.1% expression? Need identify single numerical result replication registered target. Paper title/main finding CLDN18.2 defines subgroup via CD8 exclusion. Headline numerical result perhaps CLDN18.2 exclusively expressed in 24.1% (20/83) of ICC tissues. The wording conclusion: \"this study establishes CLDN18.2 as a tumor-specific biomarker in ICC, expressed in 24.1% of ICC patients with absent normal tissue expression.\" They ask headline number only, value paper itself states, unit paper prints. Evidence exact contiguous quote contains number, if linked by wording quote whole clause. Need choose number and unit. parent_value number 24.1, unit \"%\" likely. Evidence exact contiguous quotation: \"CLDN18.2 was exclusively expressed in 24.1% (20/83) of ICC tissues, absent in non-tumor tissues.\" This is exact sentence, contains attribution and main result. target_result perhaps concise \"24.1%\" or \"CLDN18.2 was exclusively expressed in 24.1% of ICC tissues.\" Since headline number only maybe parent_value 24.1, unit \"%\". target_result could \"24.1%\" or descriptive. Need not include converted count. Evidence whole clause due linked directly. Need ensure quote exact contiguous source. Yes.\n\nCould registered target instead be HR 2.555 for reduced OS, the headline numerical result for main finding? Need reason. They explicitly define target as \"the headline numerical result the paper states for its main finding.\" In source, first result and conclusion emphasize expression prevalence 24.1%. Main title finding includes prognostic subgroup and CD8 exclusion, but no single exact headline beyond 24.1%. The instruction likely asks extraction benchmark where target generic, identify main numerical result. Usually abstracts have one headline number. Here likely 24.1% because conclusion repeats it. Need perhaps evidence quote whole conclusion clause: \"In conclusion, this study establishes CLDN18.2 as a tumor-specific biomarker in ICC, expressed in 24.1% of ICC patients with absent normal tissue expression.\" This explicitly labels main finding. Better than result sentence. They demand \"When that is how text links them, quote whole clause so reader can check attribution.\" We can quote entire exact sentence. Does evidence need only clause containing number? Exact contiguous. Use conclusion sentence. Unit printed \"%\" embedded. parent_value 24.1. target_result perhaps \"24.1% of ICC patients\" (headline number only asks report headline number only, perhaps target_result should just \"24.1%\"). JSON schema target_result string. We can say \"24.1%\" to comply headline number only, while evidence quote. They ask \"Report the headline number only: the value...\" So target_result likely \"24.1%\". Other fields required. Let's formulate.\n\nNeed valid JSON no markdown. Ensure Unicode okay. Evidence exact:\n\"In conclusion, this study establishes CLDN18.2 as a tumor-specific biomarker in ICC, expressed in 24.1% of ICC patients with absent normal tissue expression.\"\nYes source exact. Could unit \"%\" and parent_value 24.1. number_stated true.\n\nLet's answer.</think>\n\n{\"parent_value\":24.1,\"unit\":\"%\",\"evidence\":\"In conclusion, this study establishes CLDN18.2 as a tumor-specific biomarker in ICC, expressed in 24.1% of ICC patients with absent normal tissue expression.\",\"target_result\":\"24.1%\",\"number_stated\":true}", "reading": {"parent_value": 24.1, "unit": "%", "evidence": "In conclusion, this study establishes CLDN18.2 as a tumor-specific biomarker in ICC, expressed in 24.1% of ICC patients with absent normal tissue expression.", "target_result": "24.1%", "number_stated": true, "source_locator": "chars 5176-5333 of source sha256 dcb877d871ba2b34be8a8c832ec4e28918193a4d85570cb6f3d69ec264ad7b63"}, "recorded_at": "2026-10-31T15:36:06.297212+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "CLDN18.2 expression was an independent prognostic factor for reduced overall survival (OS: HR = 2.555, 95% CI = 1.250–5.223, P = 0.01).", "minimax_alt": "Multivariable analysis identified CLDN18.2 as an independent prognostic factor for reduced overall survival (OS: HR = 2.555, 95% CI = 1.250–5.223, P = 0.01) and disease-free survival (DFS: HR = 2.229, 95% CI = 1.125–4.415, P = 0.022).", "decisive": false}, "physical_methods": {"minimax": ["Tissue microarray immunohistochemistry (IHC)", "CD8+ tumor-infiltrating lymphocyte (TIL) quantification"], "minimax_alt": ["Immunohistochemistry (IHC) on tissue microarray sections from 83 ICC and 47 matched non-tumor tissues", "CD8+ tumor-infiltrating lymphocyte (TIL) quantification"], "decisive": false}, "analysis_methods": {"minimax": ["Single-sample gene set enrichment analysis (ssGSEA)", "TIMER method in the IOBR R package", "Kaplan-Meier method", "Log-rank test", "Cox proportional hazards regression"], "minimax_alt": ["Single-sample gene set enrichment analysis (ssGSEA)", "TIMER method in the IOBR R package", "Wilcoxon rank-sum test", "chi-square test", "Fisher's exact test", "one-sample t-test", "one-way ANOVA", "Kaplan-Meier method", "log-rank test", "univariate and multivariate Cox proportional hazards regression"], "decisive": false}, "statistical_method": {"minimax": "Cox proportional hazards regression", "minimax_alt": "Multivariable Cox proportional hazards regression", "decisive": true}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:91c5e09e7a2593656663c98008024767d70a37641cfa6f2fcea7a8dc302a67fd", "type": "sep_package", "label": "SEP v1 package for pmid:40951359"}], "activities": [{"id": "activity:conversion:pmid:40951359", "type": "conversion", "used": ["package:91c5e09e7a2593656663c98008024767d70a37641cfa6f2fcea7a8dc302a67fd"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40951359", "parent_hash": "sha256:bd7d6a92ad049c3211250ad193d8dc223da4165687ec8a7670c0474b8acd8c8e", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40951359 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40951359' does not resolve to a declared asset", "targets"]}