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pmid:40650680

Single-cell RNA sequencing and multi-omics analysis of prognosis-related staging in papillary thyroid cancer.

Cancer immunology, immunotherapy : CII · 2025 doi:10.1007/s00262-025-04101-4

Paper

partial

Experiment

partial

Data

partial

Analysis

absent

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
sci_version
1.0
id
pmid:40650680
kind
science-record
revision
2
content_hash
sha256:17182d56c7f00156085266ec811328b5517522e1aa595277044ae2caed91eee4
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:51Z
updated_at
2026-11-01T14:01:44Z
generator object · 3 fields
name
corpus-assay-engine
converter
sep_to_sci_v1
source_package_schema
urn:bntrg:sep:1.0.0
paper object · 10 fields
state
partial
title
Single-cell RNA sequencing and multi-omics analysis of prognosis-related staging in papillary thyroid cancer.
doi
10.1007/s00262-025-04101-4
pmid
40650680
authors
null
journal
Cancer immunology, immunotherapy : CII
year
2025
abstract
null
claims array · 1 item
[0] object · 6 fields
id
claim-1
statement
the headline numerical result the paper states for its main finding
kind
quantitative
state
complete
target object · 4 fields
value
21.511
unit
multivariate hr
tolerance
null
source
chars 1483-1597 of source sha256 8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40650680
locator
chars 1483-1597 of source sha256 8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316
quote
A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P < 0.001).
gaps array · 2 items
[0]
abstract
[1]
authors
experiment object · 8 fields
state
partial
objective
the headline numerical result the paper states for its main finding
steps array · 3 items
[0] object · 13 fields
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 object · 0 fields
inputs array · 1 item
[0]
source:pmid:40650680
outputs array · 1 item
[0]
the published estimate, its unit and its interval
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
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 object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the source data with its provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
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:40650680
duration_hours
null
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the registered result
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 3 items
[0]
step:obtain_source_data blocked on data:not_downloaded
[1]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[2]
step:run_analysis input 'materials:the source data behind the published result in pmid:40650680' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:40650680
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1007/s00262-025-04101-4
sha256
sha256:8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316
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null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1007/s00262-025-04101-4
version
null
note
Source read by the package builder: full_text.
structure object · 1 field
access_state
full_text
[1] object · 16 fields
id
asset:table:pmid:40650680:1
role
table
format
jats-table
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application/vnd.jats.table+json
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null
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sha256:5b9888a8a47f1facb98908605f6816fe94360fc83785da862649fe60ba76823b
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2367
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verified
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read_table
reader_status
available
identifier
section[18]/table-wrap[1]#Tab1
version
null
note
Differences in clinical prognostic features among 48 PTC patients categorized into high- and low-risk groups
structure object · 5 fields
pmcid
PMC12255609
section_index
18
section_title
Experimental validation cohort stratification for PCR analysis
row_count
37
column_count
6
table object · 8 fields
label
Table 1
caption
Differences in clinical prognostic features among 48 PTC patients categorized into high- and low-risk groups
rows array · 37 items
[0] array · 6 items
[0]
Variables
[1]
Total (n = 48)
[2]
High risk (n = 25)
[3]
Low risk (n = 23)
[4]
Statistic
[5]
P
[1] array · 6 items
[0]
Age, Mean ± SD (yrs)
[1]
46.94 ± 12.82
[2]
51.08 ± 12.63
[3]
42.43 ± 11.67
[4]
t = 2.47
[5]
0.017
[2] array · 6 items
[0]
Size, Mean ± SD (cm)
[1]
2.18 ± 2.20
[2]
2.79 ± 2.70
[3]
1.51 ± 1.22
[4]
t = 2.15
[5]
0.039
[3] array · 6 items
[0]
Lymph node metastasis rate, Mean ± SD
[1]
0.45 ± 0.36
[2]
0.49 ± 0.37
[3]
0.41 ± 0.34
[4]
t = 0.71
[5]
0.483
[4] array · 6 items
[0]
Gender, n (%)
[1]
[2]
[3]
[4]
χ2 = 0.68
[5]
0.410
[5] array · 6 items
[0]
Female
[1]
29 (60.42)
[2]
17 (68.00)
[3]
12 (52.17)
[4]
[5]
[6] array · 6 items
[0]
Male
[1]
19 (39.58)
[2]
8 (32.00)
[3]
11 (47.83)
[4]
[5]
[7] array · 6 items
[0]
Multiple foci, n (%)
[1]
[2]
[3]
[4]
χ2 = 0.05
[5]
0.815
[8] array · 6 items
[0]
No
[1]
29 (60.42)
[2]
16 (64.00)
[3]
13 (56.52)
[4]
[5]
[9] array · 6 items
[0]
Yes
[1]
19 (39.58)
[2]
9 (36.00)
[3]
10 (43.48)
[4]
[5]
[10] array · 6 items
[0]
Thyroiditis, n (%)
[1]
[2]
[3]
[4]
χ2 = 0.27
[5]
0.602
[11] array · 6 items
[0]
No
[1]
30 (62.50)
[2]
17 (68.00)
[3]
13 (56.52)
[4]
[5]
[12] array · 6 items
[0]
Yes
[1]
18 (37.50)
[2]
8 (32.00)
[3]
10 (43.48)
[4]
[5]
[13] array · 6 items
[0]
Thyroid nodules, n (%)
[1]
[2]
[3]
[4]
χ2 = 0.31
[5]
0.578
[14] array · 6 items
[0]
No
[1]
22 (45.83)
[2]
10 (40.00)
[3]
12 (52.17)
[4]
[5]
[15] array · 6 items
[0]
Yes
[1]
26 (54.17)
[2]
15 (60.00)
[3]
11 (47.83)
[4]
[5]
[16] array · 6 items
[0]
KRAS mutations, n (%)
[1]
[2]
[3]
[4]
–
[5]
1.000
[17] array · 6 items
[0]
No
[1]
48 (100.00)
[2]
25 (100.00)
[3]
23 (100.00)
[4]
[5]
[18] array · 6 items
[0]
Yes
[1]
0 (0.00)
[2]
0 (0.00)
[3]
0 (0.00)
[4]
[5]
[19] array · 6 items
[0]
BRAF mutations, n (%)
[1]
[2]
[3]
[4]
χ2 = 0.00
[5]
1.000
[20] array · 6 items
[0]
No
[1]
5 (10.42)
[2]
3 (12.00)
[3]
2 (8.70)
[4]
[5]
[21] array · 6 items
[0]
Yes
[1]
43 (89.58)
[2]
22 (88.00)
[3]
21 (91.30)
[4]
[5]
[22] array · 6 items
[0]
TERT mutations, n (%)
[1]
[2]
[3]
[4]
χ2 = 0.00
[5]
1.000
[23] array · 6 items
[0]
No
[1]
46 (95.83)
[2]
24 (96.00)
[3]
22 (95.65)
[4]
[5]
[24] array · 6 items
[0]
Yes
[1]
2 (4.17)
[2]
1 (4.00)
[3]
1 (4.35)
[4]
[5]
[25] array · 6 items
[0]
Recurrent, n (%)
[1]
[2]
[3]
[4]
χ2 = 7.40
[5]
0.007
[26] array · 6 items
[0]
No
[1]
29 (60.42)
[2]
10 (40.00)
[3]
19 (82.61)
[4]
[5]
[27] array · 6 items
[0]
Yes
[1]
19 (39.58)
[2]
15 (60.00)
[3]
4 (17.39)
[4]
[5]
[28] array · 6 items
[0]
TPO, n (%)
[1]
[2]
[3]
[4]
χ2 = 0.00
[5]
1.000
[29] array · 6 items
[0]
Negative
[1]
46 (95.83)
[2]
24 (96.00)
[3]
22 (95.65)
[4]
[5]
[30] array · 6 items
[0]
Positive
[1]
2 (4.17)
[2]
1 (4.00)
[3]
1 (4.35)
[4]
[5]
[31] array · 6 items
[0]
HBME-1, n (%)
[1]
[2]
[3]
[4]
χ2 = 0.02
[5]
0.875
[32] array · 6 items
[0]
Negative
[1]
11 (22.92)
[2]
5 (20.00)
[3]
6 (26.09)
[4]
[5]
[33] array · 6 items
[0]
Positive
[1]
37 (77.08)
[2]
20 (80.00)
[3]
17 (73.91)
[4]
[5]
[34] array · 6 items
[0]
CD56, n (%)
[1]
[2]
[3]
[4]
χ2 = 0.00
[5]
1.000
[35] array · 6 items
[0]
Negative
[1]
45 (93.75)
[2]
23 (92.00)
[3]
22 (95.65)
[4]
[5]
[36] array · 6 items
[0]
Positive
[1]
3 (6.25)
[2]
2 (8.00)
[3]
1 (4.35)
[4]
[5]
row_count
37
column_count
6
numeric_cells
107
header_rows
1
locator
section[18]/table-wrap[1]#Tab1
gaps array · 1 item
[0]
asset:source:pmid:40650680 not verified
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
targets
capability object · 3 fields
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absent
requirements array · 0 items
gaps array · 1 item
[0]
capability
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state
partial
tier
null
blocking_axis
null
blocked_on
null
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
[0]
source:pmid:40650680
[1]
asset:table:pmid:40650680:1
steps array · 1 item
[0]
read_published_estimate
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
[0]
xml
capabilities array · 0 items
data_gaps array · 1 item
[0]
source:pmid:40650680
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
passed
providers array · 2 items
[0] object · 7 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
full-text-reading-v1
prompt_hash
e1dd29742d2ec6017c62365c0677e424c18535b02d130f33cb9c4078baedf70a
source_hash
8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316
raw_response_sha256
sha256:ba0c578ddd7e39c1f143e0e6135ab9bbc576cc4084c292f0130259599dbafd5f
raw_response_chars
6043
[1] object · 7 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
full-text-reading-v1
prompt_hash
3f1a4c83b8484a2382ac2e4595e49acddf4cf9ea4fba9a70bfca53e496988815
source_hash
8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316
raw_response_sha256
sha256:feedfcf9b452386162e729dfbc474d9ee1a9cf037d6ede808bdc0d1bdb5062cc
raw_response_chars
54302
target_providers array · 2 items
[0] object · 8 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
replication-target-v2
prompt_hash
8758bf0f60460b3768a96ffcd7f2857ca0d26fc537563ae05fe0898bc4bcfc62
source_hash
8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316
raw_response
{"parent_value":21.511,"unit":"multivariate HR","evidence":"A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P < 0.001).","target_result":"The 7-gene risk score independently predicted prognosis with a multivariate HR of 21.511 (P < 0.001).","number_stated":true}
reading object · 6 fields
parent_value
21.511
unit
multivariate HR
evidence
A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P < 0.001).
target_result
The 7-gene risk score independently predicted prognosis with a multivariate HR of 21.511 (P < 0.001).
number_stated
true
source_locator
chars 1483-1597 of source sha256 8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316
recorded_at
2026-10-31T15:19:28.970125+00:00
[1] object · 8 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
replication-target-v2
prompt_hash
36810404d4d0bdf8d2132467d7aa4d2a9cb41f6d79161f979dab730b2e4ba0e2
source_hash
8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316
raw_response
<think>We need answer JSON only. Need identify single numerical result replication registered target headline main finding. Need infer likely headline number: multivariate HR = 21.511? Paper abstract states "A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P &lt; 0.001)." Target headline numerical result paper states for main finding. Need report value paper itself states, unit printed. Number 21.511, unit likely "multivariate HR" or "HR"? Prompt headline number only, unit must unit paper prints. They ask JSON parent_value numeric, unit string, evidence exact contiguous quote containing number, whole clause attribution. Could be 21.511, unit "multivariate HR". Evidence exact quote perhaps "A 7-gene risk score derived from MCD&amp;PRGs independently predicted prognosis (multivariate HR = 21.511, P &lt; 0.001)." target_result perhaps concise description. Need ensure registered target "headline numerical result paper states for its main finding". There are many numbers (34 gene, 3 subtypes, PFS P, 7 gene, HR, n=48 recurrence P). Main headline numerical result likely HR=21.511. Need output exactly JSON valid. Unit "multivariate HR" perhaps hazard ratio dimensionless. The printed unit is HR, with modifier multivariate. Asked "unit must be the unit the paper prints." Could use "multivariate HR". Evidence exact contiguous. Maybe headline number should be 21.511. target_result string can state "The 7-gene risk score independently predicted prognosis." Ensure no invented source. Let's formulate. Could ambiguity: "single numerical result that a replication of registered target has to reproduce" means registered target main finding, and paper headline number maybe 21.511. Yes. JSON: {"parent_value":21.511,"unit":"multivariate HR","evidence":"A 7-gene risk score derived from MCD&amp;PRGs independently predicted prognosis (multivariate HR = 21.511, P &lt; 0.001).","target_result":"The 7-gene risk score derived from MCD&amp;PRGs independently predicted prognosis.","number_stated":true} Need perhaps unit "HR" only. They say report headline number only: value. Unit must paper prints. "multivariate HR = 21.511" is not unit exactly perhaps unit "HR". target result captures. I'd set unit "HR" because the statistical metric's unit/label. Yet "multivariate HR" is printed wording. Schema parent_value likely numerical result and unit.</think> {"parent_value":21.511,"unit":"multivariate HR","evidence":"A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P < 0.001).","target_result":"The 7-gene risk score derived from MCD&PRGs independently predicted prognosis.","number_stated":true}
reading object · 6 fields
parent_value
21.511
unit
multivariate HR
evidence
A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P < 0.001).
target_result
The 7-gene risk score derived from MCD&PRGs independently predicted prognosis.
number_stated
true
source_locator
chars 1483-1597 of source sha256 8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316
recorded_at
2026-10-31T15:19:33.148020+00:00
agreement
true
disagreements object · 2 fields
physical_methods object · 3 fields
minimax array · 1 item
[0]
qRT-PCR validation in an independent institutional cohort using key markers (DEPTOR, APOE, APOC1)
minimax_alt array · 1 item
[0]
quantitative real-time PCR (qRT-PCR)
decisive
false
analysis_methods object · 3 fields
minimax array · 11 items
[0]
single-cell RNA sequencing
[1]
bulk-RNA sequencing
[2]
multi-omics analysis
[3]
consensus clustering
[4]
principal component analysis
[5]
Kaplan–Meier survival analysis
[6]
Cox proportional hazards regression
[7]
ANOVA
[8]
t tests
[9]
Chi-squared tests
[10]
correlation analyses
minimax_alt array · 6 items
[0]
Single-cell RNA sequencing (scRNA-seq)
[1]
bulk-RNA sequencing multi-omics integration
[2]
consensus clustering
[3]
principal component analysis (PCA)
[4]
Kaplan–Meier survival analysis
[5]
Cox proportional hazards regression
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
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not_run
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null
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null
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false
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null
stages array · 7 items
[0] object · 4 fields
key
target_materials
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pending
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null
evidence
null
[1] object · 4 fields
key
independent_readings
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passed
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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
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null
evidence
null
[3] object · 4 fields
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protocol_reconstruction
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pending
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null
evidence
null
[4] object · 4 fields
key
control_execution
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pending
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null
evidence
null
[5] object · 4 fields
key
control_comparison
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pending
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null
evidence
null
[6] object · 4 fields
key
publication
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null
evidence
null
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[0]
review.human_critique
[1]
review.machine_critique.passed
execution object · 5 fields
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[0]
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id
package:48ad15020a887ecd2a6e5928738b33b957c0e5a99033db79ef9a0a9b7d53beaa
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sep_package
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SEP v1 package for pmid:40650680
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[0] object · 4 fields
id
activity:conversion:pmid:40650680
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conversion
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[0]
package:48ad15020a887ecd2a6e5928738b33b957c0e5a99033db79ef9a0a9b7d53beaa
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agent:corpus-assay-engine
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agent:minimax
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minimax
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agent:minimax_alt
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minimax_alt
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agent:corpus-assay-engine
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343fb30756ba6ec3
capability_table_fingerprint
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lineage object · 4 fields
parent_id
pmid:40650680
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null
generation
2
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:40650680 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
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[7]
review.human_critique
[8]
review.machine_critique.passed
[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:40650680' 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:40650680", "kind": "science-record", "revision": 2, "content_hash": "sha256:17182d56c7f00156085266ec811328b5517522e1aa595277044ae2caed91eee4", "created_at": "2026-11-01T10:25:51Z", "updated_at": "2026-11-01T14:01:44Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Single-cell RNA sequencing and multi-omics analysis of prognosis-related staging in papillary thyroid cancer.", "doi": "10.1007/s00262-025-04101-4", "pmid": "40650680", "authors": null, "journal": "Cancer immunology, immunotherapy : CII", "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": 21.511, "unit": "multivariate hr", "tolerance": null, "source": "chars 1483-1597 of source sha256 8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316"}, "evidence": [{"asset": "source:pmid:40650680", "locator": "chars 1483-1597 of source sha256 8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316", "quote": "A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P < 0.001)."}]}], "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:40650680"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, 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[], "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:40650680' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40650680", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s00262-025-04101-4", "sha256": "sha256:8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s00262-025-04101-4", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40650680:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5b9888a8a47f1facb98908605f6816fe94360fc83785da862649fe60ba76823b", "bytes": 2367, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#Tab1", "version": null, "note": "Differences in clinical prognostic features among 48 PTC patients categorized into high- and low-risk groups", "structure": {"pmcid": "PMC12255609", "section_index": 18, "section_title": "Experimental validation cohort stratification for PCR analysis", "row_count": 37, "column_count": 6}, "table": {"label": "Table 1", "caption": "Differences in clinical prognostic features among 48 PTC patients categorized into high- and low-risk groups", "rows": [["Variables", "Total (n = 48)", "High risk (n = 25)", "Low risk (n = 23)", "Statistic", "P"], ["Age, Mean ± SD (yrs)", "46.94 ± 12.82", "51.08 ± 12.63", "42.43 ± 11.67", "t = 2.47", "0.017"], ["Size, Mean ± SD (cm)", "2.18 ± 2.20", "2.79 ± 2.70", "1.51 ± 1.22", "t = 2.15", "0.039"], ["Lymph node metastasis rate, Mean ± SD", "0.45 ± 0.36", "0.49 ± 0.37", "0.41 ± 0.34", "t = 0.71", "0.483"], ["Gender, n (%)", "", "", "", "χ2 = 0.68", "0.410"], ["Female", "29 (60.42)", "17 (68.00)", "12 (52.17)", "", ""], ["Male", "19 (39.58)", "8 (32.00)", "11 (47.83)", "", ""], ["Multiple foci, n (%)", "", "", "", "χ2 = 0.05", "0.815"], ["No", "29 (60.42)", "16 (64.00)", "13 (56.52)", "", ""], ["Yes", "19 (39.58)", "9 (36.00)", "10 (43.48)", "", ""], ["Thyroiditis, n (%)", "", "", "", "χ2 = 0.27", "0.602"], ["No", "30 (62.50)", "17 (68.00)", "13 (56.52)", "", ""], ["Yes", "18 (37.50)", "8 (32.00)", "10 (43.48)", "", ""], ["Thyroid nodules, n (%)", "", "", "", "χ2 = 0.31", "0.578"], ["No", "22 (45.83)", "10 (40.00)", "12 (52.17)", "", ""], ["Yes", "26 (54.17)", "15 (60.00)", "11 (47.83)", "", ""], ["KRAS mutations, n (%)", "", "", "", "–", "1.000"], ["No", "48 (100.00)", "25 (100.00)", "23 (100.00)", "", ""], ["Yes", "0 (0.00)", "0 (0.00)", "0 (0.00)", "", ""], ["BRAF mutations, n (%)", "", "", "", "χ2 = 0.00", "1.000"], ["No", "5 (10.42)", "3 (12.00)", "2 (8.70)", "", ""], ["Yes", "43 (89.58)", "22 (88.00)", "21 (91.30)", "", ""], ["TERT mutations, n (%)", "", "", "", "χ2 = 0.00", "1.000"], ["No", "46 (95.83)", "24 (96.00)", "22 (95.65)", "", ""], ["Yes", "2 (4.17)", "1 (4.00)", "1 (4.35)", "", ""], ["Recurrent, n (%)", "", "", "", "χ2 = 7.40", "0.007"], ["No", "29 (60.42)", "10 (40.00)", "19 (82.61)", "", ""], ["Yes", "19 (39.58)", "15 (60.00)", "4 (17.39)", "", ""], ["TPO, n (%)", "", "", "", "χ2 = 0.00", "1.000"], ["Negative", "46 (95.83)", "24 (96.00)", "22 (95.65)", "", ""], ["Positive", "2 (4.17)", "1 (4.00)", "1 (4.35)", "", ""], ["HBME-1, n (%)", "", "", "", "χ2 = 0.02", "0.875"], ["Negative", "11 (22.92)", "5 (20.00)", "6 (26.09)", "", ""], ["Positive", "37 (77.08)", "20 (80.00)", "17 (73.91)", "", ""], ["CD56, n (%)", "", "", "", "χ2 = 0.00", "1.000"], ["Negative", "45 (93.75)", "23 (92.00)", "22 (95.65)", "", ""], ["Positive", "3 (6.25)", "2 (8.00)", "1 (4.35)", "", ""]], "row_count": 37, "column_count": 6, "numeric_cells": 107, "header_rows": 1, "locator": "section[18]/table-wrap[1]#Tab1"}}], "gaps": ["asset:source:pmid:40650680 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:40650680", "asset:table:pmid:40650680:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40650680"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "passed", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "e1dd29742d2ec6017c62365c0677e424c18535b02d130f33cb9c4078baedf70a", "source_hash": "8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316", "raw_response_sha256": "sha256:ba0c578ddd7e39c1f143e0e6135ab9bbc576cc4084c292f0130259599dbafd5f", "raw_response_chars": 6043}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "3f1a4c83b8484a2382ac2e4595e49acddf4cf9ea4fba9a70bfca53e496988815", "source_hash": "8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316", "raw_response_sha256": "sha256:feedfcf9b452386162e729dfbc474d9ee1a9cf037d6ede808bdc0d1bdb5062cc", "raw_response_chars": 54302}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "8758bf0f60460b3768a96ffcd7f2857ca0d26fc537563ae05fe0898bc4bcfc62", "source_hash": "8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316", "raw_response": "{\"parent_value\":21.511,\"unit\":\"multivariate HR\",\"evidence\":\"A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P < 0.001).\",\"target_result\":\"The 7-gene risk score independently predicted prognosis with a multivariate HR of 21.511 (P < 0.001).\",\"number_stated\":true}", "reading": {"parent_value": 21.511, "unit": "multivariate HR", "evidence": "A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P < 0.001).", "target_result": "The 7-gene risk score independently predicted prognosis with a multivariate HR of 21.511 (P < 0.001).", "number_stated": true, "source_locator": "chars 1483-1597 of source sha256 8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316"}, "recorded_at": "2026-10-31T15:19:28.970125+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "36810404d4d0bdf8d2132467d7aa4d2a9cb41f6d79161f979dab730b2e4ba0e2", "source_hash": "8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316", "raw_response": "<think>We need answer JSON only. Need identify single numerical result replication registered target headline main finding. Need infer likely headline number: multivariate HR = 21.511? Paper abstract states \"A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P &lt; 0.001).\" Target headline numerical result paper states for main finding. Need report value paper itself states, unit printed. Number 21.511, unit likely \"multivariate HR\" or \"HR\"? Prompt headline number only, unit must unit paper prints. They ask JSON parent_value numeric, unit string, evidence exact contiguous quote containing number, whole clause attribution. Could be 21.511, unit \"multivariate HR\". Evidence exact quote perhaps \"A 7-gene risk score derived from MCD&amp;PRGs independently predicted prognosis (multivariate HR = 21.511, P &lt; 0.001).\" target_result perhaps concise description. Need ensure registered target \"headline numerical result paper states for its main finding\". There are many numbers (34 gene, 3 subtypes, PFS P, 7 gene, HR, n=48 recurrence P). Main headline numerical result likely HR=21.511. Need output exactly JSON valid. Unit \"multivariate HR\" perhaps hazard ratio dimensionless. The printed unit is HR, with modifier multivariate. Asked \"unit must be the unit the paper prints.\" Could use \"multivariate HR\". Evidence exact contiguous. Maybe headline number should be 21.511. target_result string can state \"The 7-gene risk score independently predicted prognosis.\" Ensure no invented source. Let's formulate.\n\nCould ambiguity: \"single numerical result that a replication of registered target has to reproduce\" means registered target main finding, and paper headline number maybe 21.511. Yes.\n\nJSON:\n{\"parent_value\":21.511,\"unit\":\"multivariate HR\",\"evidence\":\"A 7-gene risk score derived from MCD&amp;PRGs independently predicted prognosis (multivariate HR = 21.511, P &lt; 0.001).\",\"target_result\":\"The 7-gene risk score derived from MCD&amp;PRGs independently predicted prognosis.\",\"number_stated\":true}\n\nNeed perhaps unit \"HR\" only. They say report headline number only: value. Unit must paper prints. \"multivariate HR = 21.511\" is not unit exactly perhaps unit \"HR\". target result captures. I'd set unit \"HR\" because the statistical metric's unit/label. Yet \"multivariate HR\" is printed wording. Schema parent_value likely numerical result and unit.</think>\n\n{\"parent_value\":21.511,\"unit\":\"multivariate HR\",\"evidence\":\"A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P < 0.001).\",\"target_result\":\"The 7-gene risk score derived from MCD&PRGs independently predicted prognosis.\",\"number_stated\":true}", "reading": {"parent_value": 21.511, "unit": "multivariate HR", "evidence": "A 7-gene risk score derived from MCD&PRGs independently predicted prognosis (multivariate HR = 21.511, P < 0.001).", "target_result": "The 7-gene risk score derived from MCD&PRGs independently predicted prognosis.", "number_stated": true, "source_locator": "chars 1483-1597 of source sha256 8a7e96dd37c75f560e048796cfa0d833e620014265fd8ea0e93a188f3fa53316"}, "recorded_at": "2026-10-31T15:19:33.148020+00:00"}], "agreement": true, "disagreements": {"physical_methods": {"minimax": ["qRT-PCR validation in an independent institutional cohort using key markers (DEPTOR, APOE, APOC1)"], "minimax_alt": ["quantitative real-time PCR (qRT-PCR)"], "decisive": false}, "analysis_methods": {"minimax": ["single-cell RNA sequencing", "bulk-RNA sequencing", "multi-omics analysis", "consensus clustering", "principal component analysis", "Kaplan–Meier survival analysis", "Cox proportional hazards regression", "ANOVA", "t tests", "Chi-squared tests", "correlation analyses"], "minimax_alt": ["Single-cell RNA sequencing (scRNA-seq)", "bulk-RNA sequencing multi-omics integration", "consensus clustering", "principal component analysis (PCA)", "Kaplan–Meier survival analysis", "Cox proportional hazards regression"], "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": "passed", "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.passed"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:48ad15020a887ecd2a6e5928738b33b957c0e5a99033db79ef9a0a9b7d53beaa", "type": "sep_package", "label": "SEP v1 package for pmid:40650680"}], "activities": [{"id": "activity:conversion:pmid:40650680", "type": "conversion", "used": ["package:48ad15020a887ecd2a6e5928738b33b957c0e5a99033db79ef9a0a9b7d53beaa"], "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:40650680", "parent_hash": "sha256:38612333545f6e0cea0e6f7f82ffd3ffdb619e1d76c8bd7c843431ede515776b", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40650680 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.passed", "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:40650680' does not resolve to a declared asset", "targets"]}