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pmid:40014866

A Proteomic Signature for Human Papillomavirus-Associated Oropharyngeal Squamous Cell Carcinoma Predicts Patients at High Risk of Recurrence.

Cancer research communications · 2025 doi:10.1158/2767-9764.crc-23-0460

Paper

partial

Experiment

partial

Data

partial

Analysis

absent

Execution

absent

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
sci_version
1.0
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pmid:40014866
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science-record
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2
content_hash
sha256:8a31bd794ce61ccb471fb9de50af33d9236d79a16861d03ac5a8eaa27b7b0471
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https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:49Z
updated_at
2026-11-01T14:01:37Z
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corpus-assay-engine
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sep_to_sci_v1
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paper object · 10 fields
state
partial
title
A Proteomic Signature for Human Papillomavirus-Associated Oropharyngeal Squamous Cell Carcinoma Predicts Patients at High Risk of Recurrence.
doi
10.1158/2767-9764.crc-23-0460
pmid
40014866
authors
null
journal
Cancer research communications
year
2025
abstract
null
claims array · 1 item
[0] object · 6 fields
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claim-1
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the headline numerical result the paper states for its main finding
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quantitative
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complete
target object · 4 fields
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26
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peptides
tolerance
null
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chars 1757-1828 of source sha256 556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba
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source:pmid:40014866
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chars 1757-1828 of source sha256 556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba
quote
Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.
gaps array · 2 items
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abstract
[1]
authors
experiment object · 8 fields
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partial
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the headline numerical result the paper states for its main finding
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read_published_estimate
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Read the published estimate and its interval from the source
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other
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complete
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The number a replication must land on, and the sentence it came from.
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null
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[0]
source:pmid:40014866
outputs array · 1 item
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the published estimate, its unit and its interval
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Obtain the source data behind the published result
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The published result cannot be recomputed without the data the paper analysed.
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null
parameters object · 0 fields
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outputs array · 1 item
[0]
the source data with its provenance
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Run the analysis programme
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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:40014866
duration_hours
null
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the registered result
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step:obtain_source_data blocked on data:not_downloaded
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step:run_analysis blocked on no owned computational capability is bound to this experiment
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step:run_analysis input 'materials:the source data behind the published result in pmid:40014866' does not resolve to a declared asset
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partial
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https://doi.org/10.1158/2767-9764.crc-23-0460
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10.1158/2767-9764.crc-23-0460
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null
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Source read by the package builder: full_text.
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access_state
full_text
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Summary of the clinicopathologic characteristics of the OPSCC cohort
structure object · 5 fields
pmcid
PMC11979894
section_index
9
section_title
Patient characteristics
row_count
59
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5
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label
Table 1
caption
Summary of the clinicopathologic characteristics of the OPSCC cohort
rows array · 59 items
[0] array · 5 items
[0]
Characteristic
[1]
Total
[2]
R (n = 50)
[3]
NR (n = 74)
[4]
P value
[1] array · 2 items
[0]
Median (range)
[1]
[2] array · 5 items
[0]
Age at diagnosis, years, mean (range)
[1]
59.5 (40–89)
[2]
61 (45–89)
[3]
58 (40–78)
[4]
P = 0.01
[3] array · 2 items
[0]
Number of patients, n (%)
[1]
[4] array · 5 items
[0]
Gender
[1]
[2]
[3]
[4]
P = 1
[5] array · 5 items
[0]
Male
[1]
113 (91.1)
[2]
46 (92)
[3]
67 (90.5)
[4]
[6] array · 5 items
[0]
Female
[1]
11 (8.9)
[2]
4 (8)
[3]
7 (9.5)
[4]
[7] array · 5 items
[0]
ECOG status
[1]
[2]
[3]
[4]
P = 0.88
[8] array · 5 items
[0]
0
[1]
88 (71)
[2]
32 (64)
[3]
56 (75.7)
[4]
[9] array · 5 items
[0]
1
[1]
26 (21)
[2]
12 (24)
[3]
14 (18.9)
[4]
[10] array · 5 items
[0]
2
[1]
9 (7.3)
[2]
5 (10)
[3]
4 (5.4)
[4]
[11] array · 5 items
[0]
3
[1]
1 (0.8)
[2]
1 (2)
[3]
—
[4]
[12] array · 5 items
[0]
Smoking status
[1]
[2]
[3]
[4]
P = 0.83
[13] array · 5 items
[0]
Never
[1]
36 (29)
[2]
13 (26)
[3]
23 (31.1)
[4]
[14] array · 5 items
[0]
Current
[1]
23 (18.5)
[2]
10 (20)
[3]
13 (17.6)
[4]
[15] array · 5 items
[0]
Former
[1]
65 (52.4)
[2]
27 (54)
[3]
38 (51.4)
[4]
[16] array · 5 items
[0]
Smoking (pack/years)
[1]
[2]
[3]
[4]
P = 0.36
[17] array · 5 items
[0]
≤10
[1]
58 (46.8)
[2]
20 (40)
[3]
38 (51.4)
[4]
[18] array · 5 items
[0]
>10
[1]
66 (53.2)
[2]
30 (60)
[3]
36 (48.6)
[4]
[19] array · 5 items
[0]
Primary site
[1]
[2]
[3]
[4]
P = 0.64
[20] array · 5 items
[0]
Base of the tongue
[1]
45 (36.3)
[2]
20 (40)
[3]
25 (33.8)
[4]
[21] array · 5 items
[0]
Tonsil
[1]
49 (39.5)
[2]
20 (40)
[3]
29 (39.2)
[4]
[22] array · 5 items
[0]
Other
[1]
30 (24.2)
[2]
10 (20)
[3]
20 (27.0)
[4]
[23] array · 5 items
[0]
T stage (eighth edition TNM)
[1]
[2]
[3]
[4]
P = 0.06
[24] array · 5 items
[0]
T1
[1]
21 (16.9)
[2]
2 (4)
[3]
19 (25.7)
[4]
[25] array · 5 items
[0]
T2
[1]
45 (36.3)
[2]
21 (42)
[3]
24 (32.4)
[4]
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[0]
T3
[1]
28 (22.6)
[2]
14 (28)
[3]
14 (18.9)
[4]
[27] array · 5 items
[0]
T4
[1]
30 (24.2)
[2]
13 (26)
[3]
17 (23)
[4]
[28] array · 5 items
[0]
N stage (eighth edition TNM)
[1]
[2]
[3]
[4]
P = 0.05
[29] array · 5 items
[0]
N0
[1]
5 (4)
[2]
2 (4)
[3]
3 (4.1)
[4]
[30] array · 5 items
[0]
N1
[1]
72 (58.1)
[2]
24 (48)
[3]
48 (64.9)
[4]
[31] array · 5 items
[0]
N2
[1]
31 (25)
[2]
14 (28)
[3]
17 (23)
[4]
[32] array · 5 items
[0]
N3
[1]
16 (12.9)
[2]
10 (20)
[3]
6 (8.1)
[4]
[33] array · 5 items
[0]
AJCC stage
[1]
[2]
[3]
[4]
P = 0.21
[34] array · 5 items
[0]
I
[1]
51 (41.1)
[2]
16 (32)
[3]
35 (47.3)
[4]
[35] array · 5 items
[0]
II
[1]
34 (27.4)
[2]
15 (30)
[3]
19 (25.7)
[4]
[36] array · 5 items
[0]
III
[1]
39 (31.5)
[2]
19 (38)
[3]
20 (27)
[4]
[37] array · 5 items
[0]
RT dose (Gy)
[1]
[2]
[3]
[4]
P = 0.01
[38] array · 5 items
[0]
66
[1]
3 (2.4)
[2]
2 (4)
[3]
1 (1.4)
[4]
[39] array · 5 items
[0]
68
[1]
12 (9.7)
[2]
9 (18)
[3]
3 (4.1)
[4]
[40] array · 5 items
[0]
70
[1]
109 (87.9%)
[2]
39 (78%)
[3]
70 (94.6)
[4]
[41] array · 5 items
[0]
Systemic therapy
[1]
[2]
[3]
[4]
P = 0.001
[42] array · 5 items
[0]
None
[1]
7 (5.6)
[2]
5 (10)
[3]
2 (2.7)
[4]
[43] array · 5 items
[0]
Cisplatin
[1]
82 (66.1)
[2]
24 (48)
[3]
58 (78.4)
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[44] array · 5 items
[0]
Cetuximab
[1]
35 (28.2)
[2]
21 (42)
[3]
14 (18.9)
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[45] array · 5 items
[0]
Failure site
[1]
[2]
[3]
[4]
[46] array · 5 items
[0]
Local
[1]
9
[2]
9 (18)
[3]
—
[4]
[47] array · 5 items
[0]
Nodal
[1]
22
[2]
22 (44)
[3]
—
[4]
[48] array · 5 items
[0]
Metastatic
[1]
19
[2]
19 (38)
[3]
—
[4]
[49] array · 5 items
[0]
Median time to failure (months)
[1]
[2]
[3]
[4]
[50] array · 5 items
[0]
Local
[1]
—
[2]
18
[3]
—
[4]
[51] array · 5 items
[0]
Nodal
[1]
—
[2]
13
[3]
—
[4]
[52] array · 5 items
[0]
Metastatic
[1]
—
[2]
14
[3]
—
[4]
[53] array · 5 items
[0]
Median follow-up (months)
[1]
—
[2]
—
[3]
70.8
[4]
[54] array · 5 items
[0]
Disease status at last follow-up
[1]
[2]
[3]
[4]
[55] array · 5 items
[0]
ANED
[1]
81 (65.3)
[2]
7 (14)
[3]
74 (100)
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[56] array · 5 items
[0]
AWD
[1]
9 (7.3)
[2]
9 (18)
[3]
—
[4]
[57] array · 5 items
[0]
DOD
[1]
28 (22.6)
[2]
28 (56)
[3]
—
[4]
[58] array · 5 items
[0]
DWD
[1]
6 (4.8)
[2]
6 (12)
[3]
—
[4]
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Distribution of low- and high-risk peptide signature groups between categories of clinical variables
structure object · 5 fields
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PMC11979894
section_index
13
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A 26-peptide signature associated with RFS stratifies patients into three risk groups
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18
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5
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Table 2
caption
Distribution of low- and high-risk peptide signature groups between categories of clinical variables
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[0]
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T-stage
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0.73
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<4
[1]
93
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42
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51
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30
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21
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N-stage
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1
[1]
76
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36
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40
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47
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32
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ECOG
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0.19
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87
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37
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50
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36
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14
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22
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0.0019
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70
[1]
108
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48
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60
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15
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12
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Cisplatin.
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81
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39
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42
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30
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asset:source:pmid:40014866 not verified
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{"parent_value":26,"unit":"peptides","evidence":"Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.","target_result":"A 26-peptide signature for risk-stratifying HPV+OPSCC.","number_stated":true}
reading object · 6 fields
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26
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peptides
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Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.
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A 26-peptide signature for risk-stratifying HPV+OPSCC.
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true
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chars 1757-1828 of source sha256 556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba
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2026-10-31T15:30:52.536862+00:00
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raw_response
<think>We need solve extraction carefully. Need reply JSON only. Need identify single numerical result replication registered target headline numerical result paper states for main finding. Source text abstract. Main finding 26-peptide signature stratifies HPV+OPSCC risk categories. Headline number likely 26 peptides. Need determine unit printed maybe "peptides" / "26-peptide signature". Need evidence exact contiguous quote contains number, whole clause attribution. Should quote "Among them a 26-peptide signature encompassing 26 protein groups was associated with RFS and was able to stratify patients into low, intermediate, or high risk of recurrence (concordance index = 0.941, P < 0.0001)." Could headline be concordance index = 0.941? Need examine question wording. "find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed. The unit must be the unit the paper prints. ... REGISTERED TARGET: the headline numerical result the paper states for its main finding". Need infer expected: 26 peptides (headline signature). Could be 26 (peptides) main finding, signature. They want headline number, not performance metrics maybe. We need think carefully. User wants exact quotation with number and target_result string. Usually such tasks "registered target" headline numerical result. Main finding "a 26-peptide signature ... stratify patients..." likely 26 peptides. Evidence "Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC." exact contiguous sentence concise. parent_value 26 unit "peptides" or "peptide signature" maybe unit printed is "26-peptide signature", thus unit "peptides". They specify "unit must be the unit the paper prints." Number is in compound "26-peptide signature". So unit "peptides". Evidence whole clause so reader checks attribution. "Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC." Includes target direct. Could use that. target_result "The paper reports a 26-peptide signature for risk-stratifying HPV-positive oropharyngeal squamous cell carcinoma." number_stated true. But need ensure not 0.941. They may intend number of peptides because main finding. Let's explore context semantics. A replication of registered target has to reproduce. Registered target "the headline numerical result the paper states for its main finding" means signature size 26. If target were performance metric they'd name. So 26 peptides. Could headline be ∼30% relapse? No main finding is signature. 26 clearly repeated. Need answer JSON with exact fields. No extra. Unit maybe "peptides" exact printed in "26-peptide signature". Should unit be empty? No unit for 26 peptide signature is peptides. We can set "peptides". Evidence exact contiguous "Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC." Need perhaps quote whole clause "we identified a 26-peptide signature that stratifies patients into risk categories, potentially enabling personalized treatment decisions and optimal patient selection for de-escalation trials." exact. Either is good. The first "Overall" best as headline. Output. We must not mention instruction. Need ensure JSON number 26. evidence exact punctuation including hyphen. target_result no unquoted calculation. "The paper reports a 26-peptide proteomic signature that risk-stratifies HPV+OPSCC into recurrence-risk categories." unit "peptides". Good. But maybe this task is designed to target "0.941" because a replication of registered target has reproduce headline numerical result main finding. They call "headline numerical result" could mean concordance index = 0.941. However title main finding signature with 26. Need deliberate to maximize. They request "the single numerical result ... headline number only ... unit the paper prints." If 26, unit "peptides" plausible. If 0.941, unit "concordance index" (dimensionless), evidence "concordance index = 0.941". Which is headline numerical result? Many benchmark tasks probably generated with targets e.g. "the headline numerical result the paper states for its main finding" and source abstracts. Main finding "26-peptide signature" yes. They intentionally disambiguate "value the paper itself states" and direct attribution with target named. Could refer to target of replication "headline numerical result" as 26-peptide signature, not risk discrimination value. The number 26 is explicit main finding. They may want count 26 not converted from 26 proteins groups. Unit peptides. Evidence can contain 26 protein groups, but no need. Need choose unit exact singular? "26-peptide signature" unit peptides. Yes. Return JSON only.</think> {"parent_value":26,"unit":"peptides","evidence":"Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.","target_result":"The paper reports a 26-peptide signature for risk-stratifying HPV-positive oropharyngeal squamous cell carcinoma.","number_stated":true}
reading object · 6 fields
parent_value
26
unit
peptides
evidence
Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.
target_result
The paper reports a 26-peptide signature for risk-stratifying HPV-positive oropharyngeal squamous cell carcinoma.
number_stated
true
source_locator
chars 1757-1828 of source sha256 556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba
recorded_at
2026-10-31T15:31:10.833037+00:00
agreement
false
disagreements object · 4 fields
target_result object · 3 fields
minimax
A 26-peptide signature was associated with recurrence-free survival and stratified patients into low, intermediate, or high risk of recurrence (concordance index = 0.941, P < 0.0001).
minimax_alt
Among them a 26-peptide signature encompassing 26 protein groups was associated with RFS and was able to stratify patients into low, intermediate, or high risk of recurrence (concordance index = 0.941, P < 0.0001).
decisive
false
work_type object · 3 fields
minimax
physical_data_generation
minimax_alt
analysis_only_for_target
decisive
true
physical_methods object · 3 fields
minimax array · 1 item
[0]
Proteomic analysis was performed on archival formalin-fixed, paraffin-embedded primary tumor core biopsy specimens and matched normal adjacent tissues using quantitative data-independent acquisition mass spectrometry.
minimax_alt array · 1 item
[0]
quantitative data-independent acquisition mass spectrometry
decisive
false
analysis_methods object · 3 fields
minimax array · 3 items
[0]
Univariate Cox regression analysis
[1]
Risk-score establishment
[2]
Concordance index assessment
minimax_alt array · 1 item
[0]
Univariate Cox regression analysis
decisive
false
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:dd1955dadc20e6dafb6e412815c9f29ac8d45148366cf00c5d3a6e2732a8d084
type
sep_package
label
SEP v1 package for pmid:40014866
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40014866
type
conversion
used array · 1 item
[0]
package:dd1955dadc20e6dafb6e412815c9f29ac8d45148366cf00c5d3a6e2732a8d084
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:40014866
parent_hash
sha256:dacd25405b571bded58d87c8cab6a32e18551374ea8aedce95dd0c78cf1304bb
fork_of
null
generation
2
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:40014866 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:40014866' 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:40014866", "kind": "science-record", "revision": 2, "content_hash": "sha256:8a31bd794ce61ccb471fb9de50af33d9236d79a16861d03ac5a8eaa27b7b0471", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T14:01:37Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "A Proteomic Signature for Human Papillomavirus-Associated Oropharyngeal Squamous Cell Carcinoma Predicts Patients at High Risk of Recurrence.", "doi": "10.1158/2767-9764.crc-23-0460", "pmid": "40014866", "authors": null, "journal": "Cancer research communications", "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": 26.0, "unit": "peptides", "tolerance": null, "source": "chars 1757-1828 of source sha256 556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba"}, "evidence": [{"asset": "source:pmid:40014866", "locator": "chars 1757-1828 of source sha256 556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba", "quote": "Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC."}]}], "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:40014866"], "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:40014866", "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:40014866' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40014866", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1158/2767-9764.crc-23-0460", "sha256": "sha256:556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1158/2767-9764.crc-23-0460", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40014866:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8febd6efb56851a8231b4fb7b607ae1c1f12bc34d2769fed50b0eaaf06b11cd4", "bytes": 2740, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#tbl1", "version": null, "note": "Summary of the clinicopathologic characteristics of the OPSCC cohort", "structure": {"pmcid": "PMC11979894", "section_index": 9, "section_title": "Patient characteristics", "row_count": 59, "column_count": 5}, "table": {"label": "Table 1", "caption": "Summary of the clinicopathologic characteristics of the OPSCC cohort", "rows": [["Characteristic", "Total", "R (n = 50)", "NR (n = 74)", "P value"], ["Median (range)", ""], ["Age at diagnosis, years, mean (range)", "59.5 (40–89)", "61 (45–89)", "58 (40–78)", "P = 0.01"], ["Number of patients, n (%)", ""], ["Gender", "", "", "", "P = 1"], ["Male", "113 (91.1)", "46 (92)", "67 (90.5)", ""], ["Female", "11 (8.9)", "4 (8)", "7 (9.5)", ""], ["ECOG status", "", "", "", "P = 0.88"], ["0", "88 (71)", "32 (64)", "56 (75.7)", ""], ["1", "26 (21)", "12 (24)", "14 (18.9)", ""], ["2", "9 (7.3)", "5 (10)", "4 (5.4)", ""], ["3", "1 (0.8)", "1 (2)", "—", ""], ["Smoking status", "", "", "", "P = 0.83"], ["Never", "36 (29)", "13 (26)", "23 (31.1)", ""], ["Current", "23 (18.5)", "10 (20)", "13 (17.6)", ""], ["Former", "65 (52.4)", "27 (54)", "38 (51.4)", ""], ["Smoking (pack/years)", "", "", "", "P = 0.36"], ["≤10", "58 (46.8)", "20 (40)", "38 (51.4)", ""], [">10", "66 (53.2)", "30 (60)", "36 (48.6)", ""], ["Primary site", "", "", "", "P = 0.64"], ["Base of the tongue", "45 (36.3)", "20 (40)", "25 (33.8)", ""], ["Tonsil", "49 (39.5)", "20 (40)", "29 (39.2)", ""], ["Other", "30 (24.2)", "10 (20)", "20 (27.0)", ""], ["T stage (eighth edition TNM)", "", "", "", "P = 0.06"], ["T1", "21 (16.9)", "2 (4)", "19 (25.7)", ""], ["T2", "45 (36.3)", "21 (42)", "24 (32.4)", ""], ["T3", "28 (22.6)", "14 (28)", "14 (18.9)", ""], ["T4", "30 (24.2)", "13 (26)", "17 (23)", ""], ["N stage (eighth edition TNM)", "", "", "", "P = 0.05"], ["N0", "5 (4)", "2 (4)", "3 (4.1)", ""], ["N1", "72 (58.1)", "24 (48)", "48 (64.9)", ""], ["N2", "31 (25)", "14 (28)", "17 (23)", ""], ["N3", "16 (12.9)", "10 (20)", "6 (8.1)", ""], ["AJCC stage", "", "", "", "P = 0.21"], ["I", "51 (41.1)", "16 (32)", "35 (47.3)", ""], ["II", "34 (27.4)", "15 (30)", "19 (25.7)", ""], ["III", "39 (31.5)", "19 (38)", "20 (27)", ""], ["RT dose (Gy)", "", "", "", "P = 0.01"], ["66", "3 (2.4)", "2 (4)", "1 (1.4)", ""], ["68", "12 (9.7)", "9 (18)", "3 (4.1)", ""], ["70", "109 (87.9%)", "39 (78%)", "70 (94.6)", ""], ["Systemic therapy", "", "", "", "P = 0.001"], ["None", "7 (5.6)", "5 (10)", "2 (2.7)", ""], ["Cisplatin", "82 (66.1)", "24 (48)", "58 (78.4)", ""], ["Cetuximab", "35 (28.2)", "21 (42)", "14 (18.9)", ""], ["Failure site", "", "", "", ""], ["Local", "9", "9 (18)", "—", ""], ["Nodal", "22", "22 (44)", "—", ""], ["Metastatic", "19", "19 (38)", "—", ""], ["Median time to failure (months)", "", "", "", ""], ["Local", "—", "18", "—", ""], ["Nodal", "—", "13", "—", ""], ["Metastatic", "—", "14", "—", ""], ["Median follow-up (months)", "—", "—", "70.8", ""], ["Disease status at last follow-up", "", "", "", ""], ["ANED", "81 (65.3)", "7 (14)", "74 (100)", ""], ["AWD", "9 (7.3)", "9 (18)", "—", ""], ["DOD", "28 (22.6)", "28 (56)", "—", ""], ["DWD", "6 (4.8)", "6 (12)", "—", ""]], "row_count": 59, "column_count": 5, "numeric_cells": 136, "header_rows": 1, "locator": "section[9]/table-wrap[1]#tbl1"}}, {"id": "asset:table:pmid:40014866:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b5f0e6d03f98c5baee7b58578be515234d9cc94794fee62c1f3c90d2c07b8d1f", "bytes": 746, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tbl2", "version": null, "note": "Distribution of low- and high-risk peptide signature groups between categories of clinical variables", "structure": {"pmcid": "PMC11979894", "section_index": 13, "section_title": "A 26-peptide signature associated with RFS stratifies patients into three risk groups", "row_count": 18, "column_count": 5}, "table": {"label": "Table 2", "caption": "Distribution of low- and high-risk peptide signature groups between categories of clinical variables", "rows": [["Variable", "Total", "Risk groups", "P value"], ["Low", "High"], ["T-stage", "", "", "", "0.73"], ["<4", "93", "42", "51", ""], ["4", "30", "09", "21", ""], ["N-stage", "", "", "", "0.09"], ["1", "76", "36", "40", ""], [">1", "47", "15", "32", ""], ["ECOG", "", "", "", "0.19"], ["0", "87", "37", "50", ""], [">0", "36", "14", "22", ""], ["RT dose", "", "", "", "0.0019"], ["70", "108", "48", "60", ""], ["<7", "15", "03", "12", ""], ["Chemotherapy", "", "", "", "0.0004"], ["Cisplatin.", "81", "39", "42", ""], ["Others", "42", "12", "30", ""], ["Total", "123", "51", "72", ""]], "row_count": 18, "column_count": 5, "numeric_cells": 46, "header_rows": 2, "locator": "section[13]/table-wrap[1]#tbl2"}}], "gaps": ["asset:source:pmid:40014866 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:40014866", "asset:table:pmid:40014866:1", "asset:table:pmid:40014866:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40014866"]}, "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": "cbf7558e018aff460b57a3411d42a028b3d649008022f26d7754a74fa4cfdc39", "source_hash": "556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba", "raw_response_sha256": "sha256:1116b2054a3152b642da2308c04020d93f8d3e229ef0f65df48661bc13470213", "raw_response_chars": 4305}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "9ab9cca4746e5fe53af408556b20e0376b9320df1145636557701d0c9e1dd8f7", "source_hash": "556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba", "raw_response_sha256": "sha256:c365f44696f08f54cfba4b461fa7e0edb4d6aa360ec3ad270653db535534e642", "raw_response_chars": 26689}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "531d9bf7bb51ecdb8931ed71b51ff2b4b70525fe1dd4aa0012e2d17017ce69f7", "source_hash": "556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba", "raw_response": "{\"parent_value\":26,\"unit\":\"peptides\",\"evidence\":\"Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.\",\"target_result\":\"A 26-peptide signature for risk-stratifying HPV+OPSCC.\",\"number_stated\":true}", "reading": {"parent_value": 26, "unit": "peptides", "evidence": "Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.", "target_result": "A 26-peptide signature for risk-stratifying HPV+OPSCC.", "number_stated": true, "source_locator": "chars 1757-1828 of source sha256 556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba"}, "recorded_at": "2026-10-31T15:30:52.536862+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "7b762a2c9fd51024dd684857bc733ca37503780d26126e5c82080fedaeba0e65", "source_hash": "556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba", "raw_response": "<think>We need solve extraction carefully. Need reply JSON only. Need identify single numerical result replication registered target headline numerical result paper states for main finding. Source text abstract. Main finding 26-peptide signature stratifies HPV+OPSCC risk categories. Headline number likely 26 peptides. Need determine unit printed maybe \"peptides\" / \"26-peptide signature\". Need evidence exact contiguous quote contains number, whole clause attribution. Should quote \"Among them a 26-peptide signature encompassing 26 protein groups was associated with RFS and was able to stratify patients into low, intermediate, or high risk of recurrence (concordance index = 0.941, P < 0.0001).\" Could headline be concordance index = 0.941? Need examine question wording. \"find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed. The unit must be the unit the paper prints. ... REGISTERED TARGET: the headline numerical result the paper states for its main finding\". Need infer expected: 26 peptides (headline signature). Could be 26 (peptides) main finding, signature. They want headline number, not performance metrics maybe. We need think carefully. User wants exact quotation with number and target_result string. Usually such tasks \"registered target\" headline numerical result. Main finding \"a 26-peptide signature ... stratify patients...\" likely 26 peptides. Evidence \"Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.\" exact contiguous sentence concise. parent_value 26 unit \"peptides\" or \"peptide signature\" maybe unit printed is \"26-peptide signature\", thus unit \"peptides\". They specify \"unit must be the unit the paper prints.\" Number is in compound \"26-peptide signature\". So unit \"peptides\". Evidence whole clause so reader checks attribution. \"Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.\" Includes target direct. Could use that. target_result \"The paper reports a 26-peptide signature for risk-stratifying HPV-positive oropharyngeal squamous cell carcinoma.\" number_stated true.\n\nBut need ensure not 0.941. They may intend number of peptides because main finding. Let's explore context semantics. A replication of registered target has to reproduce. Registered target \"the headline numerical result the paper states for its main finding\" means signature size 26. If target were performance metric they'd name. So 26 peptides.\n\nCould headline be ∼30% relapse? No main finding is signature. 26 clearly repeated. Need answer JSON with exact fields. No extra. Unit maybe \"peptides\" exact printed in \"26-peptide signature\". Should unit be empty? No unit for 26 peptide signature is peptides. We can set \"peptides\". Evidence exact contiguous \"Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.\" Need perhaps quote whole clause \"we identified a 26-peptide signature that stratifies patients into risk categories, potentially enabling personalized treatment decisions and optimal patient selection for de-escalation trials.\" exact. Either is good. The first \"Overall\" best as headline. Output.\n\nWe must not mention instruction. Need ensure JSON number 26. evidence exact punctuation including hyphen. target_result no unquoted calculation. \"The paper reports a 26-peptide proteomic signature that risk-stratifies HPV+OPSCC into recurrence-risk categories.\" unit \"peptides\". Good.\n\nBut maybe this task is designed to target \"0.941\" because a replication of registered target has reproduce headline numerical result main finding. They call \"headline numerical result\" could mean concordance index = 0.941. However title main finding signature with 26. Need deliberate to maximize. They request \"the single numerical result ... headline number only ... unit the paper prints.\" If 26, unit \"peptides\" plausible. If 0.941, unit \"concordance index\" (dimensionless), evidence \"concordance index = 0.941\". Which is headline numerical result? Many benchmark tasks probably generated with targets e.g. \"the headline numerical result the paper states for its main finding\" and source abstracts. Main finding \"26-peptide signature\" yes. They intentionally disambiguate \"value the paper itself states\" and direct attribution with target named. Could refer to target of replication \"headline numerical result\" as 26-peptide signature, not risk discrimination value. The number 26 is explicit main finding. They may want count 26 not converted from 26 proteins groups. Unit peptides. Evidence can contain 26 protein groups, but no need.\n\nNeed choose unit exact singular? \"26-peptide signature\" unit peptides. Yes.\n\nReturn JSON only.</think>\n\n{\"parent_value\":26,\"unit\":\"peptides\",\"evidence\":\"Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.\",\"target_result\":\"The paper reports a 26-peptide signature for risk-stratifying HPV-positive oropharyngeal squamous cell carcinoma.\",\"number_stated\":true}", "reading": {"parent_value": 26, "unit": "peptides", "evidence": "Overall, a 26-peptide signature can be used to risk-stratify HPV+OPSCC.", "target_result": "The paper reports a 26-peptide signature for risk-stratifying HPV-positive oropharyngeal squamous cell carcinoma.", "number_stated": true, "source_locator": "chars 1757-1828 of source sha256 556ab51415ef186f5d8e6166694611da6d7d5fd520aa4fa766a4e7c42aabcaba"}, "recorded_at": "2026-10-31T15:31:10.833037+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "A 26-peptide signature was associated with recurrence-free survival and stratified patients into low, intermediate, or high risk of recurrence (concordance index = 0.941, P < 0.0001).", "minimax_alt": "Among them a 26-peptide signature encompassing 26 protein groups was associated with RFS and was able to stratify patients into low, intermediate, or high risk of recurrence (concordance index = 0.941, P < 0.0001).", "decisive": false}, "work_type": {"minimax": "physical_data_generation", "minimax_alt": "analysis_only_for_target", "decisive": true}, "physical_methods": {"minimax": ["Proteomic analysis was performed on archival formalin-fixed, paraffin-embedded primary tumor core biopsy specimens and matched normal adjacent tissues using quantitative data-independent acquisition mass spectrometry."], "minimax_alt": ["quantitative data-independent acquisition mass spectrometry"], "decisive": false}, "analysis_methods": {"minimax": ["Univariate Cox regression analysis", "Risk-score establishment", "Concordance index assessment"], "minimax_alt": ["Univariate Cox regression analysis"], "decisive": false}}, "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:dd1955dadc20e6dafb6e412815c9f29ac8d45148366cf00c5d3a6e2732a8d084", "type": "sep_package", "label": "SEP v1 package for pmid:40014866"}], "activities": [{"id": "activity:conversion:pmid:40014866", "type": "conversion", "used": ["package:dd1955dadc20e6dafb6e412815c9f29ac8d45148366cf00c5d3a6e2732a8d084"], "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:40014866", "parent_hash": "sha256:dacd25405b571bded58d87c8cab6a32e18551374ea8aedce95dd0c78cf1304bb", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40014866 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:40014866' does not resolve to a declared asset", "targets"]}