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pmid:40149517

The Impact of Tertiary Lymphoid Structures on Tumor Prognosis and the Immune Microenvironment in Colorectal Cancer.

Biomedicines · 2025 doi:10.3390/biomedicines13030539

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
id
pmid:40149517
kind
science-record
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sha256:ff26179a7584ea101b7373cc13314f1bb2d04238a902a8afb96f79eeb724c237
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https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
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2026-11-01T10:25:50Z
updated_at
2026-11-01T14:01:38Z
generator object · 3 fields
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corpus-assay-engine
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sep_to_sci_v1
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urn:bntrg:sep:1.0.0
paper object · 10 fields
state
partial
title
The Impact of Tertiary Lymphoid Structures on Tumor Prognosis and the Immune Microenvironment in Colorectal Cancer.
doi
10.3390/biomedicines13030539
pmid
40149517
authors
null
journal
Biomedicines
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
kind
quantitative
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complete
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13
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genes
tolerance
null
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chars 1132-1231 of source sha256 d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1
evidence array · 1 item
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source:pmid:40149517
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chars 1132-1231 of source sha256 d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1
quote
A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.
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[0]
abstract
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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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1
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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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null
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The number a replication must land on, and the sentence it came from.
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[0]
source:pmid:40149517
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[0]
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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the source data with its provenance
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no owned computational capability is bound to this experiment
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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:40149517
parameters object · 0 fields
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[0]
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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:40149517' does not resolve to a declared asset
data object · 3 fields
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partial
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[0] object · 15 fields
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xml
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application/xml
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section[30]/table-wrap[1]#array1
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null
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null
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PMC11940631
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30
section_title
Abbreviations
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25
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2
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null
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null
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[0] array · 2 items
[0]
CRC
[1]
colorectal cancer
[1] array · 2 items
[0]
OS
[1]
overall survival
[2] array · 2 items
[0]
TLSs
[1]
tertiary lymphoid structures
[3] array · 2 items
[0]
TME
[1]
tumor microenvironment
[4] array · 2 items
[0]
DCs
[1]
dendritic cells
[5] array · 2 items
[0]
HEVs
[1]
high endothelial venules
[6] array · 2 items
[0]
CRLMs
[1]
colorectal liver metastases
[7] array · 2 items
[0]
TCGA
[1]
The Cancer Genome Atlas
[8] array · 2 items
[0]
GEO
[1]
Gene Expression Omnibus
[9] array · 2 items
[0]
RNA-seq
[1]
RNA sequencing
[10] array · 2 items
[0]
GO
[1]
Gene Ontology
[11] array · 2 items
[0]
KEGG
[1]
Kyoto Encyclopedia of Genes and Genomes
[12] array · 2 items
[0]
KM
[1]
Kaplan–Meier
[13] array · 2 items
[0]
ssGSEA
[1]
single-sample gene set enrichment analysis
[14] array · 2 items
[0]
stage
[1]
tumor stage
[15] array · 2 items
[0]
T
[1]
tumor size and local invasion
[16] array · 2 items
[0]
N
[1]
lymph node involvement
[17] array · 2 items
[0]
M
[1]
metastasis
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[0]
ANOVA
[1]
analysis of variance
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[0]
CC
[1]
cellular component
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[0]
BP
[1]
biological process
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[0]
MF
[1]
molecular function
[22] array · 2 items
[0]
TMB
[1]
tumor mutational burden
[23] array · 2 items
[0]
NK
[1]
natural killer
[24] array · 2 items
[0]
ICB
[1]
immune checkpoint blockade
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section[30]/table-wrap[1]#array1
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[0]
asset:source:pmid:40149517 not verified
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source:pmid:40149517
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asset:table:pmid:40149517:1
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read_published_estimate
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xml
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source:pmid:40149517
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corpus_record_absent
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{"parent_value":13,"unit":"genes","evidence":"A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.","target_result":"13-gene TLS-associated prognostic model for colorectal cancer","number_stated":true}
reading object · 6 fields
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13
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genes
evidence
A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.
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13-gene TLS-associated prognostic model for colorectal cancer
number_stated
true
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chars 1132-1231 of source sha256 d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1
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2026-10-31T15:36:21.523094+00:00
[1] object · 8 fields
provider
minimax_alt
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MiniMax-M3
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d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1
raw_response
<think>We need answer JSON only. Need interpret task. Need find single numerical result replication registered target headline numerical result paper states for main finding, value stated not calculated. Target is main finding. Source abstract says "A 13-gene TLS-associated prognostic model for CRC was developed" likely headline numerical result 13 genes. But elsewhere says 11 genes, conclusions 10 genes. Need determine registered target headline numerical result paper states for main finding. Asked "headline numerical result the paper states for its main finding". Likely value 13, unit genes, evidence exact contiguous quote containing number, perhaps whole clause. We need report headline number only. Number stated true. Evidence exact contiguous quote. Maybe "A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes." Unit "genes". parent_value 13. target_result maybe perhaps "A 13-gene TLS-associated prognostic model for CRC was developed." But instruction "Report the headline number only" perhaps target_result should be concise. JSON schema includes target_result. We need populate likely "13-gene TLS-associated prognostic model for CRC" or numerical result statement. Evidence quote whole clause. Exact quote: "A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes." This is contiguous and directly target. Unit paper prints? It prints "13-gene", unit genes. Could use "genes". Need make sure "registered target" perhaps asks headline numerical result, singular. Could it instead be 582 sample cohort? The "main finding" is prognostic model, headline result likely 13-gene model. Abstract results starts exact. The paper inconsistent (11 genes in section, 10 conclusion), but registered target wants headline number, likely abstract's 13. We should not calculate. Output valid JSON. Could target_result be "13-gene TLS-associated prognostic model for CRC" but headline number only might mean value only and unit separately. target_result perhaps "The paper states a 13-gene TLS-associated prognostic model for CRC." Evidence. Let's formulate no extra. Ensure evidence exact punctuation. JSON escaping not issue.</think> {"parent_value":13,"unit":"genes","evidence":"A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.","target_result":"A 13-gene TLS-associated prognostic model for CRC was developed.","number_stated":true}
reading object · 6 fields
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13
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genes
evidence
A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.
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A 13-gene TLS-associated prognostic model for CRC was developed.
number_stated
true
source_locator
chars 1132-1231 of source sha256 d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1
recorded_at
2026-10-31T15:36:16.347912+00:00
agreement
false
disagreements object · 3 fields
target_result object · 3 fields
minimax
A 13-gene TLS-associated prognostic model for colorectal cancer was developed, and the TLS-high group exhibited significantly better outcomes than the TLS-low group.
minimax_alt
A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes. Survival analysis indicated significantly better outcomes for the TLS-high group.
decisive
false
analysis_methods object · 3 fields
minimax array · 3 items
[0]
Cox regression analysis
[1]
Kaplan-Meier survival analysis
[2]
single-sample gene set enrichment analysis (ssGSEA)
minimax_alt array · 3 items
[0]
single-sample gene set enrichment analysis (ssGSEA)
[1]
Cox regression
[2]
Kaplan-Meier survival analysis
decisive
false
statistical_method object · 3 fields
minimax
Cox regression and Kaplan-Meier survival analyses
minimax_alt
Cox and Kaplan-Meier analyses
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
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null
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null
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null
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[0] object · 4 fields
key
target_materials
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null
evidence
null
[1] object · 4 fields
key
independent_readings
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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
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key
source_resolution
status
pending
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null
evidence
null
[3] object · 4 fields
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protocol_reconstruction
status
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null
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null
[4] object · 4 fields
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control_execution
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pending
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null
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null
[5] object · 4 fields
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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
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absent
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not_run
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null
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entities array · 1 item
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id
package:61a7b5db963b96dfe378742e6447f007949bfadcbd68be0f3c0e831be1155cb4
type
sep_package
label
SEP v1 package for pmid:40149517
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40149517
type
conversion
used array · 1 item
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package:61a7b5db963b96dfe378742e6447f007949bfadcbd68be0f3c0e831be1155cb4
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minimax_alt
[2] object · 3 fields
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capability_table_fingerprint
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lineage object · 4 fields
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gaps array · 13 items
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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:40149517' does not resolve to a declared asset
[12]
targets
Complete file
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"sha256:a5f6226324779927b54ca802d1657e0c7f4fa77269d09a426ae2b8dd813295cb", "bytes": 954, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[30]/table-wrap[1]#array1", "version": null, "note": null, "structure": {"pmcid": "PMC11940631", "section_index": 30, "section_title": "Abbreviations", "row_count": 25, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["CRC", "colorectal cancer"], ["OS", "overall survival"], ["TLSs", "tertiary lymphoid structures"], ["TME", "tumor microenvironment"], ["DCs", "dendritic cells"], ["HEVs", "high endothelial venules"], ["CRLMs", "colorectal liver metastases"], ["TCGA", "The Cancer Genome Atlas"], ["GEO", "Gene Expression Omnibus"], ["RNA-seq", "RNA sequencing"], ["GO", "Gene Ontology"], ["KEGG", "Kyoto Encyclopedia of Genes and Genomes"], ["KM", "Kaplan–Meier"], ["ssGSEA", "single-sample gene set enrichment analysis"], ["stage", "tumor stage"], ["T", "tumor size and local invasion"], ["N", "lymph node involvement"], ["M", "metastasis"], ["ANOVA", "analysis of variance"], ["CC", "cellular component"], ["BP", "biological process"], ["MF", "molecular function"], ["TMB", "tumor mutational burden"], ["NK", "natural killer"], ["ICB", "immune checkpoint blockade"]], "row_count": 25, "column_count": 2, "numeric_cells": 0, "header_rows": 0, "locator": "section[30]/table-wrap[1]#array1"}}], "gaps": ["asset:source:pmid:40149517 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:40149517", "asset:table:pmid:40149517:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40149517"]}, "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": "7d08cf1024eb84b040363e7bbb64b42a910d8ab18e6318d709f4a5f1b2ff3a38", "source_hash": "d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1", "raw_response_sha256": "sha256:74c0effad3ff054525063fd775f0b3cde0826baea85146b02e3df547c1bfeb61", "raw_response_chars": 4501}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "44398bbab2834c294c6c5afaaa17d2e09b4a9ea5158379bd2c32a363199d4213", "source_hash": "d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1", "raw_response_sha256": "sha256:3fabded801f45d39c65d47cdbddcdda7613f5b01b553b792e46287ce7c744a21", "raw_response_chars": 58121}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "06150ff5d84966465ce8954ff558ddb075b24e8f8860155d7457d9c6ee47534b", "source_hash": "d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1", "raw_response": "{\"parent_value\":13,\"unit\":\"genes\",\"evidence\":\"A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.\",\"target_result\":\"13-gene TLS-associated prognostic model for colorectal cancer\",\"number_stated\":true}", "reading": {"parent_value": 13, "unit": "genes", "evidence": "A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.", "target_result": "13-gene TLS-associated prognostic model for colorectal cancer", "number_stated": true, "source_locator": "chars 1132-1231 of source sha256 d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1"}, "recorded_at": "2026-10-31T15:36:21.523094+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "424568f4073ab4871d293859b9624bd2bedd8310dcd5e420ed28d7de3d03cb90", "source_hash": "d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1", "raw_response": "<think>We need answer JSON only. Need interpret task. Need find single numerical result replication registered target headline numerical result paper states for main finding, value stated not calculated. Target is main finding. Source abstract says \"A 13-gene TLS-associated prognostic model for CRC was developed\" likely headline numerical result 13 genes. But elsewhere says 11 genes, conclusions 10 genes. Need determine registered target headline numerical result paper states for main finding. Asked \"headline numerical result the paper states for its main finding\". Likely value 13, unit genes, evidence exact contiguous quote containing number, perhaps whole clause. We need report headline number only. Number stated true. Evidence exact contiguous quote. Maybe \"A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.\" Unit \"genes\". parent_value 13. target_result maybe perhaps \"A 13-gene TLS-associated prognostic model for CRC was developed.\" But instruction \"Report the headline number only\" perhaps target_result should be concise. JSON schema includes target_result. We need populate likely \"13-gene TLS-associated prognostic model for CRC\" or numerical result statement. Evidence quote whole clause. Exact quote: \"A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.\" This is contiguous and directly target. Unit paper prints? It prints \"13-gene\", unit genes. Could use \"genes\". Need make sure \"registered target\" perhaps asks headline numerical result, singular. Could it instead be 582 sample cohort? The \"main finding\" is prognostic model, headline result likely 13-gene model. Abstract results starts exact. The paper inconsistent (11 genes in section, 10 conclusion), but registered target wants headline number, likely abstract's 13. We should not calculate. Output valid JSON.\n\nCould target_result be \"13-gene TLS-associated prognostic model for CRC\" but headline number only might mean value only and unit separately. target_result perhaps \"The paper states a 13-gene TLS-associated prognostic model for CRC.\" Evidence. Let's formulate no extra. Ensure evidence exact punctuation. JSON escaping not issue.</think>\n\n{\"parent_value\":13,\"unit\":\"genes\",\"evidence\":\"A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.\",\"target_result\":\"A 13-gene TLS-associated prognostic model for CRC was developed.\",\"number_stated\":true}", "reading": {"parent_value": 13, "unit": "genes", "evidence": "A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.", "target_result": "A 13-gene TLS-associated prognostic model for CRC was developed.", "number_stated": true, "source_locator": "chars 1132-1231 of source sha256 d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1"}, "recorded_at": "2026-10-31T15:36:16.347912+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "A 13-gene TLS-associated prognostic model for colorectal cancer was developed, and the TLS-high group exhibited significantly better outcomes than the TLS-low group.", "minimax_alt": "A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes. Survival analysis indicated significantly better outcomes for the TLS-high group.", "decisive": false}, "analysis_methods": {"minimax": ["Cox regression analysis", "Kaplan-Meier survival analysis", "single-sample gene set enrichment analysis (ssGSEA)"], "minimax_alt": ["single-sample gene set enrichment analysis (ssGSEA)", "Cox regression", "Kaplan-Meier survival analysis"], "decisive": false}, "statistical_method": {"minimax": "Cox regression and Kaplan-Meier survival analyses", "minimax_alt": "Cox and Kaplan-Meier analyses", "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:61a7b5db963b96dfe378742e6447f007949bfadcbd68be0f3c0e831be1155cb4", "type": "sep_package", "label": "SEP v1 package for pmid:40149517"}], "activities": [{"id": "activity:conversion:pmid:40149517", "type": "conversion", "used": ["package:61a7b5db963b96dfe378742e6447f007949bfadcbd68be0f3c0e831be1155cb4"], "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:40149517", "parent_hash": "sha256:3f48f0e0381d4e1fb5faf949800838eb36bdc4b9cf3cfbb6bd86144d98cae654", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40149517 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:40149517' does not resolve to a declared asset", "targets"]}