Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:40703507

CPLX1 is a novel prognostic biomarker in CRC correlating with immunotherapy resistance and ferroptosis.

Frontiers in immunology · 2025 doi:10.3389/fimmu.2025.1589423

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:40703507
kind
science-record
revision
2
content_hash
sha256:07f55e40f5c787d11b8c828db3cdd3140e82cf5b736075b9eebc2b37725f441d
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
CPLX1 is a novel prognostic biomarker in CRC correlating with immunotherapy resistance and ferroptosis.
doi
10.3389/fimmu.2025.1589423
pmid
40703507
authors
null
journal
Frontiers in immunology
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
qualitative
state
blocked
target object · 4 fields
value
null
unit
null
tolerance
null
source
null
evidence array · 0 items
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:40703507
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:40703507
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:40703507' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 4 items
[0] object · 15 fields
id
source:pmid:40703507
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3389/fimmu.2025.1589423
sha256
sha256:82b49560d9dcffcadfeef2bbb1480403dafbcbb38e896eee1cb563e5f5ca9bff
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3389/fimmu.2025.1589423
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:40703507:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:ae5d461a55319b96da7ef6cdb0077d03258b73033d7abf1b51676385e1bdba57
bytes
1697
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[28]/table-wrap[1]#T1
version
null
note
Clinicopathological features for CRC patients in relation to CPLX1 level.
structure object · 5 fields
pmcid
PMC12283636
section_index
28
section_title
Patients’ baseline features
row_count
36
column_count
4
table object · 8 fields
label
Table 1
caption
Clinicopathological features for CRC patients in relation to CPLX1 level.
rows array · 36 items
[0] array · 4 items
[0]
Characteristics
[1]
Low expression of CPLX1
[2]
High expression of CPLX1
[3]
P value
[1] array · 4 items
[0]
n
[1]
322
[2]
322
[3]
[2] array · 4 items
[0]
Pathologic T stage, n (%)
[1]
[2]
[3]
< 0.001
[3] array · 4 items
[0]
T1&T2
[1]
85 (13.3%)
[2]
46 (7.2%)
[3]
[4] array · 4 items
[0]
T3&T4
[1]
235 (36.7%)
[2]
275 (42.9%)
[3]
[5] array · 4 items
[0]
Pathologic N stage, n (%)
[1]
[2]
[3]
0.744
[6] array · 4 items
[0]
N0
[1]
188 (29.4%)
[2]
180 (28.1%)
[3]
[7] array · 4 items
[0]
N1
[1]
76 (11.9%)
[2]
77 (12%)
[3]
[8] array · 4 items
[0]
N2
[1]
56 (8.8%)
[2]
63 (9.8%)
[3]
[9] array · 4 items
[0]
Pathologic M stage, n (%)
[1]
[2]
[3]
0.187
[10] array · 4 items
[0]
M0
[1]
239 (42.4%)
[2]
236 (41.8%)
[3]
[11] array · 4 items
[0]
M1
[1]
38 (6.7%)
[2]
51 (9%)
[3]
[12] array · 4 items
[0]
Pathologic stage, n (%)
[1]
[2]
[3]
0.265
[13] array · 4 items
[0]
Stage I & Stage II
[1]
180 (28.9%)
[2]
169 (27.1%)
[3]
[14] array · 4 items
[0]
Stage III & Stage IV
[1]
129 (20.7%)
[2]
145 (23.3%)
[3]
[15] array · 4 items
[0]
Primary therapy outcome, n (%)
[1]
[2]
[3]
0.852
[16] array · 4 items
[0]
PD&SD
[1]
21 (6.7%)
[2]
17 (5.4%)
[3]
[17] array · 4 items
[0]
PR&CR
[1]
147 (47.1%)
[2]
127 (40.7%)
[3]
[18] array · 4 items
[0]
Gender, n (%)
[1]
[2]
[3]
0.179
[19] array · 4 items
[0]
Female
[1]
142 (22%)
[2]
159 (24.7%)
[3]
[20] array · 4 items
[0]
Male
[1]
180 (28%)
[2]
163 (25.3%)
[3]
[21] array · 4 items
[0]
Race, n (%)
[1]
[2]
[3]
0.831
[22] array · 4 items
[0]
Asian & Black or African American
[1]
43 (10.9%)
[2]
38 (9.6%)
[3]
[23] array · 4 items
[0]
White
[1]
162 (41.1%)
[2]
151 (38.3%)
[3]
[24] array · 4 items
[0]
Age, n (%)
[1]
[2]
[3]
0.750
[25] array · 4 items
[0]
<= 65
[1]
140 (21.7%)
[2]
136 (21.1%)
[3]
[26] array · 4 items
[0]
> 65
[1]
182 (28.3%)
[2]
186 (28.9%)
[3]
[27] array · 4 items
[0]
CEA level, n (%)
[1]
[2]
[3]
0.136
[28] array · 4 items
[0]
<= 5
[1]
135 (32.5%)
[2]
126 (30.4%)
[3]
[29] array · 4 items
[0]
> 5
[1]
68 (16.4%)
[2]
86 (20.7%)
[3]
[30] array · 4 items
[0]
Perineural invasion, n (%)
[1]
[2]
[3]
0.080
[31] array · 4 items
[0]
No
[1]
87 (37%)
[2]
88 (37.4%)
[3]
[32] array · 4 items
[0]
Yes
[1]
22 (9.4%)
[2]
38 (16.2%)
[3]
[33] array · 4 items
[0]
Lymphatic invasion, n (%)
[1]
[2]
[3]
0.019
[34] array · 4 items
[0]
No
[1]
187 (32.1%)
[2]
163 (28%)
[3]
[35] array · 4 items
[0]
Yes
[1]
101 (17.4%)
[2]
131 (22.5%)
[3]
row_count
36
column_count
4
numeric_cells
63
header_rows
1
locator
section[28]/table-wrap[1]#T1
[2] object · 16 fields
id
asset:table:pmid:40703507:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:8c09b3446071d24b4e77dec5e304f38a7e2c12c59695e9c8093dce278804ad28
bytes
1201
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[30]/table-wrap[1]#T2
version
null
note
Links across CPLX1 levels and CRC clinicopathological characteristics, shown through logistic regression assessment.
structure object · 5 fields
pmcid
PMC12283636
section_index
30
section_title
CPLX1 is associated with CRC clinical features
row_count
12
column_count
4
table object · 8 fields
label
Table 2
caption
Links across CPLX1 levels and CRC clinicopathological characteristics, shown through logistic regression assessment.
rows array · 12 items
[0] array · 4 items
[0]
Characteristics
[1]
Total (N)
[2]
OR (95% CI)
[3]
P value
[1] array · 4 items
[0]
Pathologic T stage (T3&T4 vs. T1&T2)
[1]
641
[2]
2.162 (1.451 – 3.222)
[3]
< 0.001
[2] array · 4 items
[0]
Pathologic N stage (N1&N2 vs. N0)
[1]
640
[2]
1.108 (0.810 – 1.516)
[3]
0.522
[3] array · 4 items
[0]
Pathologic M stage (M1 vs. M0)
[1]
564
[2]
1.359 (0.861 – 2.146)
[3]
0.188
[4] array · 4 items
[0]
Pathologic stage (Stage III & Stage IV vs. Stage I & Stage II)
[1]
623
[2]
1.197 (0.872 – 1.643)
[3]
0.265
[5] array · 4 items
[0]
Primary therapy outcome (PR&CR vs. PD&SD)
[1]
312
[2]
1.067 (0.540 – 2.111)
[3]
0.852
[6] array · 4 items
[0]
Gender (Male vs. Female)
[1]
644
[2]
0.809 (0.593 – 1.103)
[3]
0.180
[7] array · 4 items
[0]
Race (White vs. Asian & Black or African American)
[1]
394
[2]
1.055 (0.647 – 1.721)
[3]
0.831
[8] array · 4 items
[0]
Age (> 65 vs. <= 65)
[1]
644
[2]
1.052 (0.770 – 1.437)
[3]
0.750
[9] array · 4 items
[0]
CEA level (> 5 vs. <= 5)
[1]
415
[2]
1.355 (0.908 – 2.022)
[3]
0.137
[10] array · 4 items
[0]
Perineural invasion (Yes vs. No)
[1]
235
[2]
1.708 (0.934 – 3.121)
[3]
0.082
[11] array · 4 items
[0]
Lymphatic invasion (Yes vs. No)
[1]
582
[2]
1.488 (1.066 – 2.078)
[3]
0.020
row_count
12
column_count
4
numeric_cells
36
header_rows
1
locator
section[30]/table-wrap[1]#T2
[3] object · 16 fields
id
asset:table:pmid:40703507:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:ac7f0cf8841c06bf186d263bb71cd11107184894cb4c9673c31a186c83496cd4
bytes
1089
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[31]/table-wrap[1]#T3
version
null
note
Survival outcomes of patients with CRC in relation to clinicopathological features and CPLX1, shown by regression analysis.
structure object · 5 fields
pmcid
PMC12283636
section_index
31
section_title
CPLX1 as a predictor of CRC prognosis
row_count
9
column_count
7
table object · 8 fields
label
Table 3
caption
Survival outcomes of patients with CRC in relation to clinicopathological features and CPLX1, shown by regression analysis.
rows array · 9 items
[0] array · 4 items
[0]
Characteristics
[1]
HR for OS (95% CI)
[2]
HR for DSS (95% CI)
[3]
HR for PFI (95% CI)
[1] array · 6 items
[0]
Univariate analysis
[1]
Multivariate analysis
[2]
Univariate analysis
[3]
Multivariate analysis
[4]
Univariate analysis
[5]
Multivariate analysis
[2] array · 7 items
[0]
T stage (T1&T2 vs. T3&T4)
[1]
2.468
[2]
10.125
[3]
6.440
[4]
70462653.4804
[5]
3.198
[6]
1.529
[3] array · 7 items
[0]
M stage (M0 vs. M1)
[1]
3.989
[2]
0.445
[3]
7.471
[4]
0.000
[5]
5.577
[6]
0.879
[4] array · 7 items
[0]
Pathologic stage (Stage I & Stage II vs. Stage III & Stage IV)
[1]
2.988
[2]
220.407
[3]
5.716
[4]
–
[5]
2.924
[6]
27.842
[5] array · 7 items
[0]
Primary therapy outcome (PD&SD vs. PR&CR)
[1]
0.109
[2]
0.173
[3]
0.055
[4]
0.212
[5]
0.097
[6]
0.138
[6] array · 7 items
[0]
Age (<=65 vs. >65)
[1]
1.939
[2]
1.372
[3]
1.421
[4]
–
[5]
1.006
[6]
–
[7] array · 7 items
[0]
Lymphatic invasion (No vs. Yes)
[1]
2.144
[2]
2.143
[3]
3.669
[4]
3.763
[5]
2.358
[6]
1.399
[8] array · 7 items
[0]
CPLX1 (Low vs. High)
[1]
1.460
[2]
1.460
[3]
1.895
[4]
1.895
[5]
1.623
[6]
1.623
row_count
9
column_count
7
numeric_cells
43
header_rows
2
locator
section[31]/table-wrap[1]#T3
gaps array · 1 item
[0]
asset:source:pmid:40703507 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
state
absent
requirements array · 0 items
gaps array · 1 item
[0]
capability
readiness object · 8 fields
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 · 4 items
[0]
source:pmid:40703507
[1]
asset:table:pmid:40703507:1
[2]
asset:table:pmid:40703507:2
[3]
asset:table:pmid:40703507:3
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:40703507
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
blocked
providers array · 2 items
[0] object · 7 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
full-text-reading-v1
prompt_hash
5452ef9f63ddee47baa4faed82fd1f0a00a7dfa7188df7ac41ba8ee38403c8c3
source_hash
82b49560d9dcffcadfeef2bbb1480403dafbcbb38e896eee1cb563e5f5ca9bff
raw_response_sha256
sha256:3e1a9311dacedf5d4381709829889791d758f2aa605527aa5a1d17bf647fb089
raw_response_chars
4966
[1] object · 7 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
full-text-reading-v1
prompt_hash
42f27fb3bb460dde290592448beaa8dcab7246c4ca135fd6cd2d286f6d0f96f3
source_hash
82b49560d9dcffcadfeef2bbb1480403dafbcbb38e896eee1cb563e5f5ca9bff
raw_response_sha256
sha256:ced9247638a77ab34b2be67a5b12a89d3560443e63acc78846d2e354d4435989
raw_response_chars
53985
target_providers array · 2 items
[0] object · 8 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
replication-target-v2
prompt_hash
cf5247430ec2f834406cfe3dfaf0645e7b086573f50d161b17913c47d6111d0d
source_hash
82b49560d9dcffcadfeef2bbb1480403dafbcbb38e896eee1cb563e5f5ca9bff
raw_response
{"parent_value":0,"unit":"","evidence":"","target_result":"The paper states that high CPLX1 expression is significantly correlated with poor prognostic outcomes in CRC patients, but it gives no numerical value for this main finding.","number_stated":false}
reading object · 6 fields
parent_value
0
unit
evidence
target_result
The paper states that high CPLX1 expression is significantly correlated with poor prognostic outcomes in CRC patients, but it gives no numerical value for this main finding.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:22:08.587169+00:00
[1] object · 8 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
replication-target-v2
prompt_hash
8d8d5c5115984b446c2a7b3606e9079b279e37b1f36b4dce78ee27366eff0931
source_hash
82b49560d9dcffcadfeef2bbb1480403dafbcbb38e896eee1cb563e5f5ca9bff
raw_response
<think>We need answer JSON only, extract claims supplied text. Need determine if numerical headline main finding present. Source abstract etc no numerical result for headline prognostic finding. There are numbers: TIMER 2.0, GEO GSE156451, p<0.05, 1000 permutations, R 3.6.3, χ2, citations (10), Cox? None main result numerical. Thus number_stated false parent_value 0 unit empty evidence empty target_result says text states high CPLX1 expression significantly correlated with poor prognostic outcomes in CRC patients, upregulated etc no headline numeric result. Need ensure exact requested "headline number only" but no number. JSON required. Should target_result maybe "The text states that high expression levels of CPLX1 are significantly correlated with poor prognostic outcomes in CRC patients, but it reports no numerical value for this main finding." Evidence empty. Good. Need not quote evidence because false. Output valid JSON object no markdown. Ensure number parent 0. target_result not claim invent.</think> {"parent_value":0,"unit":"","evidence":"","target_result":"The text states that high expression levels of CPLX1 are significantly correlated with poor prognostic outcomes in CRC patients, but it provides no numerical value for this main finding.","number_stated":false}
reading object · 6 fields
parent_value
0
unit
evidence
target_result
The text states that high expression levels of CPLX1 are significantly correlated with poor prognostic outcomes in CRC patients, but it provides no numerical value for this main finding.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:22:08.183103+00:00
agreement
false
disagreements object · 3 fields
target_result object · 3 fields
minimax
The supplied text states that high CPLX1 expression is associated with poor prognostic outcomes in CRC patients, but it does not report a numerical headline result, effect estimate, or p-value for this finding.
minimax_alt
High CPLX1 expression is significantly correlated with poor prognostic outcomes in CRC patients; the supplied text reports no numerical effect size for this headline result.
decisive
false
analysis_methods object · 3 fields
minimax array · 6 items
[0]
Kaplan-Meier plots
[1]
log-rank assessments
[2]
univariate Cox regression
[3]
multivariate Cox regression
[4]
ssGSEA
[5]
Gene Set Enrichment Analysis (GSEA)
minimax_alt array · 11 items
[0]
Integrative RNA-seq differential-expression analysis of TCGA-COAD, TCGA-READ, and GEO GSE156451 data
[1]
TIMER 2.0 evaluation of CPLX1 expression
[2]
Kaplan-Meier plots and log-rank assessments using median CPLX1 expression as the cutoff
[3]
Univariate and multivariate Cox regression
[4]
cBioPortal and COSMIC mutational analysis
[5]
Co-expression analysis
[6]
GO and KEGG analysis in metscape
[7]
Gene Set Enrichment Analysis (GSEA) with 1000 permutations of gene sets
[8]
ssGSEA immune-infiltration analysis
[9]
t-tests and two-way ANOVA
[10]
χ2 assessments, logistic regression, Fisher’s exact test, and Wilcoxon rank-sum assessment
decisive
false
statistical_method object · 3 fields
minimax
Kaplan-Meier analysis with log-rank assessments and univariate/multivariate Cox regression
minimax_alt
Kaplan-Meier plots with log-rank assessments using median CPLX1 expression as the cutoff, together with univariate and multivariate Cox 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:738e707e31d33c32e36a3ed4c899abd8a8ad20e6277d1912d01bf37bd62a6fa7
type
sep_package
label
SEP v1 package for pmid:40703507
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40703507
type
conversion
used array · 1 item
[0]
package:738e707e31d33c32e36a3ed4c899abd8a8ad20e6277d1912d01bf37bd62a6fa7
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:40703507
parent_hash
sha256:c75b4af4bd43aa962bd8639ae4bd9d3a2e973060e379bc362a2fa166ab3fbd98
fork_of
null
generation
2
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:40703507 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:40703507' 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:40703507", "kind": "science-record", "revision": 2, "content_hash": "sha256:07f55e40f5c787d11b8c828db3cdd3140e82cf5b736075b9eebc2b37725f441d", "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": "CPLX1 is a novel prognostic biomarker in CRC correlating with immunotherapy resistance and ferroptosis.", "doi": "10.3389/fimmu.2025.1589423", "pmid": "40703507", "authors": null, "journal": "Frontiers in immunology", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "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:40703507"], "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:40703507", "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:40703507' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40703507", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2025.1589423", "sha256": "sha256:82b49560d9dcffcadfeef2bbb1480403dafbcbb38e896eee1cb563e5f5ca9bff", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2025.1589423", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40703507:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ae5d461a55319b96da7ef6cdb0077d03258b73033d7abf1b51676385e1bdba57", "bytes": 1697, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[28]/table-wrap[1]#T1", "version": null, "note": "Clinicopathological features for CRC patients in relation to CPLX1 level.", "structure": {"pmcid": "PMC12283636", "section_index": 28, "section_title": "Patients’ baseline features", "row_count": 36, "column_count": 4}, "table": {"label": "Table 1", "caption": "Clinicopathological features for CRC patients in relation to CPLX1 level.", "rows": [["Characteristics", "Low expression of CPLX1", "High expression of CPLX1", "P value"], ["n", "322", "322", ""], ["Pathologic T stage, n (%)", "", "", "< 0.001"], ["T1&T2", "85 (13.3%)", "46 (7.2%)", ""], ["T3&T4", "235 (36.7%)", "275 (42.9%)", ""], ["Pathologic N stage, n (%)", "", "", "0.744"], ["N0", "188 (29.4%)", "180 (28.1%)", ""], ["N1", "76 (11.9%)", "77 (12%)", ""], ["N2", "56 (8.8%)", "63 (9.8%)", ""], ["Pathologic M stage, n (%)", "", "", "0.187"], ["M0", "239 (42.4%)", "236 (41.8%)", ""], ["M1", "38 (6.7%)", "51 (9%)", ""], ["Pathologic stage, n (%)", "", "", "0.265"], ["Stage I & Stage II", "180 (28.9%)", "169 (27.1%)", ""], ["Stage III & Stage IV", "129 (20.7%)", "145 (23.3%)", ""], ["Primary therapy outcome, n (%)", "", "", "0.852"], ["PD&SD", "21 (6.7%)", "17 (5.4%)", ""], ["PR&CR", "147 (47.1%)", "127 (40.7%)", ""], ["Gender, n (%)", "", "", "0.179"], ["Female", "142 (22%)", "159 (24.7%)", ""], ["Male", "180 (28%)", "163 (25.3%)", ""], ["Race, n (%)", "", "", "0.831"], ["Asian & Black or African American", "43 (10.9%)", "38 (9.6%)", ""], ["White", "162 (41.1%)", "151 (38.3%)", ""], ["Age, n (%)", "", "", "0.750"], ["<= 65", "140 (21.7%)", "136 (21.1%)", ""], ["> 65", "182 (28.3%)", "186 (28.9%)", ""], ["CEA level, n (%)", "", "", "0.136"], ["<= 5", "135 (32.5%)", "126 (30.4%)", ""], ["> 5", "68 (16.4%)", "86 (20.7%)", ""], ["Perineural invasion, n (%)", "", "", "0.080"], ["No", "87 (37%)", "88 (37.4%)", ""], ["Yes", "22 (9.4%)", "38 (16.2%)", ""], ["Lymphatic invasion, n (%)", "", "", "0.019"], ["No", "187 (32.1%)", "163 (28%)", ""], ["Yes", "101 (17.4%)", "131 (22.5%)", ""]], "row_count": 36, "column_count": 4, "numeric_cells": 63, "header_rows": 1, "locator": "section[28]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:40703507:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8c09b3446071d24b4e77dec5e304f38a7e2c12c59695e9c8093dce278804ad28", "bytes": 1201, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[30]/table-wrap[1]#T2", "version": null, "note": "Links across CPLX1 levels and CRC clinicopathological characteristics, shown through logistic regression assessment.", "structure": {"pmcid": "PMC12283636", "section_index": 30, "section_title": "CPLX1 is associated with CRC clinical features", "row_count": 12, "column_count": 4}, "table": {"label": "Table 2", "caption": "Links across CPLX1 levels and CRC clinicopathological characteristics, shown through logistic regression assessment.", "rows": [["Characteristics", "Total (N)", "OR (95% CI)", "P value"], ["Pathologic T stage (T3&T4 vs. T1&T2)", "641", "2.162 (1.451 – 3.222)", "< 0.001"], ["Pathologic N stage (N1&N2 vs. N0)", "640", "1.108 (0.810 – 1.516)", "0.522"], ["Pathologic M stage (M1 vs. M0)", "564", "1.359 (0.861 – 2.146)", "0.188"], ["Pathologic stage (Stage III & Stage IV vs. Stage I & Stage II)", "623", "1.197 (0.872 – 1.643)", "0.265"], ["Primary therapy outcome (PR&CR vs. PD&SD)", "312", "1.067 (0.540 – 2.111)", "0.852"], ["Gender (Male vs. Female)", "644", "0.809 (0.593 – 1.103)", "0.180"], ["Race (White vs. Asian & Black or African American)", "394", "1.055 (0.647 – 1.721)", "0.831"], ["Age (> 65 vs. <= 65)", "644", "1.052 (0.770 – 1.437)", "0.750"], ["CEA level (> 5 vs. <= 5)", "415", "1.355 (0.908 – 2.022)", "0.137"], ["Perineural invasion (Yes vs. No)", "235", "1.708 (0.934 – 3.121)", "0.082"], ["Lymphatic invasion (Yes vs. No)", "582", "1.488 (1.066 – 2.078)", "0.020"]], "row_count": 12, "column_count": 4, "numeric_cells": 36, "header_rows": 1, "locator": "section[30]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:40703507:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ac7f0cf8841c06bf186d263bb71cd11107184894cb4c9673c31a186c83496cd4", "bytes": 1089, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[31]/table-wrap[1]#T3", "version": null, "note": "Survival outcomes of patients with CRC in relation to clinicopathological features and CPLX1, shown by regression analysis.", "structure": {"pmcid": "PMC12283636", "section_index": 31, "section_title": "CPLX1 as a predictor of CRC prognosis", "row_count": 9, "column_count": 7}, "table": {"label": "Table 3", "caption": "Survival outcomes of patients with CRC in relation to clinicopathological features and CPLX1, shown by regression analysis.", "rows": [["Characteristics", "HR for OS (95% CI)", "HR for DSS (95% CI)", "HR for PFI (95% CI)"], ["Univariate analysis", "Multivariate analysis", "Univariate analysis", "Multivariate analysis", "Univariate analysis", "Multivariate analysis"], ["T stage (T1&T2 vs. T3&T4)", "2.468", "10.125", "6.440", "70462653.4804", "3.198", "1.529"], ["M stage (M0 vs. M1)", "3.989", "0.445", "7.471", "0.000", "5.577", "0.879"], ["Pathologic stage (Stage I & Stage II vs. Stage III & Stage IV)", "2.988", "220.407", "5.716", "–", "2.924", "27.842"], ["Primary therapy outcome (PD&SD vs. PR&CR)", "0.109", "0.173", "0.055", "0.212", "0.097", "0.138"], ["Age (<=65 vs. >65)", "1.939", "1.372", "1.421", "–", "1.006", "–"], ["Lymphatic invasion (No vs. Yes)", "2.144", "2.143", "3.669", "3.763", "2.358", "1.399"], ["CPLX1 (Low vs. High)", "1.460", "1.460", "1.895", "1.895", "1.623", "1.623"]], "row_count": 9, "column_count": 7, "numeric_cells": 43, "header_rows": 2, "locator": "section[31]/table-wrap[1]#T3"}}], "gaps": ["asset:source:pmid:40703507 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:40703507", "asset:table:pmid:40703507:1", "asset:table:pmid:40703507:2", "asset:table:pmid:40703507:3"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40703507"]}, "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": "5452ef9f63ddee47baa4faed82fd1f0a00a7dfa7188df7ac41ba8ee38403c8c3", "source_hash": "82b49560d9dcffcadfeef2bbb1480403dafbcbb38e896eee1cb563e5f5ca9bff", "raw_response_sha256": "sha256:3e1a9311dacedf5d4381709829889791d758f2aa605527aa5a1d17bf647fb089", "raw_response_chars": 4966}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "42f27fb3bb460dde290592448beaa8dcab7246c4ca135fd6cd2d286f6d0f96f3", "source_hash": "82b49560d9dcffcadfeef2bbb1480403dafbcbb38e896eee1cb563e5f5ca9bff", "raw_response_sha256": "sha256:ced9247638a77ab34b2be67a5b12a89d3560443e63acc78846d2e354d4435989", "raw_response_chars": 53985}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "cf5247430ec2f834406cfe3dfaf0645e7b086573f50d161b17913c47d6111d0d", "source_hash": "82b49560d9dcffcadfeef2bbb1480403dafbcbb38e896eee1cb563e5f5ca9bff", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that high CPLX1 expression is significantly correlated with poor prognostic outcomes in CRC patients, but it gives no numerical value for this main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that high CPLX1 expression is significantly correlated with poor prognostic outcomes in CRC patients, but it gives no numerical value for this main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:22:08.587169+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "8d8d5c5115984b446c2a7b3606e9079b279e37b1f36b4dce78ee27366eff0931", "source_hash": "82b49560d9dcffcadfeef2bbb1480403dafbcbb38e896eee1cb563e5f5ca9bff", "raw_response": "<think>We need answer JSON only, extract claims supplied text. Need determine if numerical headline main finding present. Source abstract etc no numerical result for headline prognostic finding. There are numbers: TIMER 2.0, GEO GSE156451, p<0.05, 1000 permutations, R 3.6.3, χ2, citations (10), Cox? None main result numerical. Thus number_stated false parent_value 0 unit empty evidence empty target_result says text states high CPLX1 expression significantly correlated with poor prognostic outcomes in CRC patients, upregulated etc no headline numeric result. Need ensure exact requested \"headline number only\" but no number. JSON required. Should target_result maybe \"The text states that high expression levels of CPLX1 are significantly correlated with poor prognostic outcomes in CRC patients, but it reports no numerical value for this main finding.\" Evidence empty. Good.\n\nNeed not quote evidence because false. Output valid JSON object no markdown. Ensure number parent 0. target_result not claim invent.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states that high expression levels of CPLX1 are significantly correlated with poor prognostic outcomes in CRC patients, but it provides no numerical value for this main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The text states that high expression levels of CPLX1 are significantly correlated with poor prognostic outcomes in CRC patients, but it provides no numerical value for this main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:22:08.183103+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "The supplied text states that high CPLX1 expression is associated with poor prognostic outcomes in CRC patients, but it does not report a numerical headline result, effect estimate, or p-value for this finding.", "minimax_alt": "High CPLX1 expression is significantly correlated with poor prognostic outcomes in CRC patients; the supplied text reports no numerical effect size for this headline result.", "decisive": false}, "analysis_methods": {"minimax": ["Kaplan-Meier plots", "log-rank assessments", "univariate Cox regression", "multivariate Cox regression", "ssGSEA", "Gene Set Enrichment Analysis (GSEA)"], "minimax_alt": ["Integrative RNA-seq differential-expression analysis of TCGA-COAD, TCGA-READ, and GEO GSE156451 data", "TIMER 2.0 evaluation of CPLX1 expression", "Kaplan-Meier plots and log-rank assessments using median CPLX1 expression as the cutoff", "Univariate and multivariate Cox regression", "cBioPortal and COSMIC mutational analysis", "Co-expression analysis", "GO and KEGG analysis in metscape", "Gene Set Enrichment Analysis (GSEA) with 1000 permutations of gene sets", "ssGSEA immune-infiltration analysis", "t-tests and two-way ANOVA", "χ2 assessments, logistic regression, Fisher’s exact test, and Wilcoxon rank-sum assessment"], "decisive": false}, "statistical_method": {"minimax": "Kaplan-Meier analysis with log-rank assessments and univariate/multivariate Cox regression", "minimax_alt": "Kaplan-Meier plots with log-rank assessments using median CPLX1 expression as the cutoff, together with univariate and multivariate Cox 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:738e707e31d33c32e36a3ed4c899abd8a8ad20e6277d1912d01bf37bd62a6fa7", "type": "sep_package", "label": "SEP v1 package for pmid:40703507"}], "activities": [{"id": "activity:conversion:pmid:40703507", "type": "conversion", "used": ["package:738e707e31d33c32e36a3ed4c899abd8a8ad20e6277d1912d01bf37bd62a6fa7"], "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:40703507", "parent_hash": "sha256:c75b4af4bd43aa962bd8639ae4bd9d3a2e973060e379bc362a2fa166ab3fbd98", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40703507 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:40703507' does not resolve to a declared asset", "targets"]}