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pmid:40760079

Predicting head and neck cancer response to radiotherapy with a chemokine-based model.

Scientific reports · 2025 doi:10.1038/s41598-025-13346-z

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
id
pmid:40760079
kind
science-record
content_hash
sha256:8e0b4b85e2ffb3f97be946d9b776858db1c92b2c40dc81c30c025f55222e6cae
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:52Z
updated_at
2026-11-01T10:25:52Z
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
Predicting head and neck cancer response to radiotherapy with a chemokine-based model.
doi
10.1038/s41598-025-13346-z
pmid
40760079
authors
null
journal
Scientific reports
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
432
unit
patients
tolerance
null
source
chars 196-359 of source sha256 73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40760079
locator
chars 196-359 of source sha256 73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c
quote
This study aimed to develop a chemokine-based model for predicting radiosensitivity in HNSCC using a retrospective analysis of 432 patients from the TCGA database.
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.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:40760079
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.
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:40760079
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:40760079' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 1 item
[0] object · 15 fields
id
source:pmid:40760079
role
manuscript
format
xml
media_type
application/xml
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https://doi.org/10.1038/s41598-025-13346-z
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sha256:73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c
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null
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resolved
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null
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reader_required
identifier
10.1038/s41598-025-13346-z
version
null
note
Source read by the package builder: full_text.
structure object · 1 field
access_state
full_text
gaps array · 1 item
[0]
asset:source:pmid:40760079 not verified
analysis object · 4 fields
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absent
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[0]
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[1]
targets
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absent
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gaps array · 1 item
[0]
capability
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partial
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null
blocked_on
null
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 1 item
[0]
source:pmid:40760079
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:40760079
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
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partial
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blocked
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minimax
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MiniMax-M3.1-Flash
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full-text-reading-v1
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a6a66955d743436c84ba69efd3275fb6c1a3fcf1d74394cde004630b74a0b4b5
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sha256:c0f67a213e88950e137336d03653f5ee6fe76ccbf5ddf208f857eda46418aa4d
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[1] object · 7 fields
provider
minimax_alt
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MiniMax-M3
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full-text-reading-v1
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73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c
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minimax
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MiniMax-M3.1-Flash
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source_hash
73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c
raw_response
{"parent_value":432,"unit":"patients","evidence":"This study aimed to develop a chemokine-based model for predicting radiosensitivity in HNSCC using a retrospective analysis of 432 patients from the TCGA database.","target_result":"The study analyzed 432 patients from the TCGA database.","number_stated":true}
reading object · 6 fields
parent_value
432
unit
patients
evidence
This study aimed to develop a chemokine-based model for predicting radiosensitivity in HNSCC using a retrospective analysis of 432 patients from the TCGA database.
target_result
The study analyzed 432 patients from the TCGA database.
number_stated
true
source_locator
chars 196-359 of source sha256 73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c
recorded_at
2026-10-31T15:28:09.288029+00:00
[1] object · 8 fields
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minimax_alt
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61988ab0af4f9e59f39696fd0646367a0987ca5d788a1cdca225e3d51b8f3069
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73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c
raw_response
<think>We need answer JSON only. Need identify single numerical result headline main finding. Source abstract says retrospective analysis 432 patients. Registered target "headline numerical result paper states for its main finding." Likely 432 patients. Need exact contiguous quote contains number, unit printed. Evidence exact clause. parent_value 432, unit "patients". target_result perhaps "432 patients". Need ensure whether headline result could be cohort size or p&lt;0.05? Main finding numerical result perhaps 432 patients from TCGA. Prompt specifically asks "single numerical result that a replication of registered target has to reproduce" and registered target main finding. Given supplied text only abstract and methods; only salient result number is 432 patients. The target likely numerical result perhaps cohort size. Evidence exact quotation: "This study aimed to develop a chemokine-based model for predicting radiosensitivity in HNSCC using a retrospective analysis of 432 patients from the TCGA database." Unit "patients". number_stated true. target_result could state "The model was developed using a retrospective analysis of 432 patients from the TCGA database." But perhaps exact source. Need output JSON valid. Ensure evidence whole clause for attribution. Exact quote. Headline number only perhaps target_result should just be "432 patients"? They said report headline number only; schema includes target_result. We can say "432 patients". Evidence full clause. Parent value 432, unit patients.</think> {"parent_value":432,"unit":"patients","evidence":"This study aimed to develop a chemokine-based model for predicting radiosensitivity in HNSCC using a retrospective analysis of 432 patients from the TCGA database.","target_result":"432 patients","number_stated":true}
reading object · 6 fields
parent_value
432
unit
patients
evidence
This study aimed to develop a chemokine-based model for predicting radiosensitivity in HNSCC using a retrospective analysis of 432 patients from the TCGA database.
target_result
432 patients
number_stated
true
source_locator
chars 196-359 of source sha256 73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c
recorded_at
2026-10-31T15:28:10.297345+00:00
agreement
false
disagreements object · 4 fields
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minimax
In a retrospective analysis of 432 HNSCC patients, a model incorporating CXCL2, CCL28, and CCR8 expression stratified patients into radiosensitive and radioresistant groups; the radiosensitive group showed significantly improved overall survival with radiotherapy.
minimax_alt
unclear: the supplied text reports a retrospective analysis of 432 patients from the TCGA database and a CXCL2/CCL28/CCR8 model that stratified patients into radiosensitive and radioresistant groups, with significantly improved overall survival in the radiosensitive group receiving radiotherapy; no numerical effect estimate, group-specific count, hazard ratio, target-specific p value, or model-performance metric is reported for the headline finding.
decisive
false
physical_methods object · 3 fields
minimax array · 1 item
[0]
In vitro experiments using radiosensitive and radioresistant tongue squamous cell carcinoma cell lines
minimax_alt array · 1 item
[0]
In vitro experiments using radiosensitive and radioresistant Tongue squamous cell carcinoma (TSCC) cell lines
decisive
false
analysis_methods object · 3 fields
minimax array · 15 items
[0]
ESTIMATE algorithm
[1]
Single-sample Gene Set Enrichment Analysis (ssGSEA)
[2]
CIBERSORT algorithm
[3]
Gene Set Variation Analysis (GSVA)
[4]
Gene Ontology analysis
[5]
Tumor Immune Dysfunction and Exclusion (TIDE) score
[6]
Immunophenotype Scores (IPS)
[7]
pRRophetic R package
[8]
Chi-square test
[9]
Mann-Whitney U test
[10]
Kruskal-Wallis test
[11]
Pearson correlation coefficient
[12]
Spearman rank correlation coefficient
[13]
Kaplan-Meier curves
[14]
Log-rank test
minimax_alt array · 16 items
[0]
Retrospective analysis of 432 patients from the TCGA database
[1]
Chemokine-based radiosensitivity model incorporating CXCL2, CCL28, and CCR8 expression
[2]
ESTIMATE algorithm
[3]
Single-sample Gene Set Enrichment Analysis (ssGSEA)
[4]
CIBERSORT
[5]
Gene Set Variation Analysis (GSVA) for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment
[6]
Gene Ontology (GO) analysis
[7]
Tumor Immune Dysfunction and Exclusion (TIDE) score
[8]
Immunophenotype Scores (IPS) for CTLA-4 and PD-1 blockade
[9]
pRRophetic R package with Genomics of Drug Sensitivity in Cancer (GDSC) data
[10]
Chi-square test
[11]
Mann-Whitney U test
[12]
Kruskal-Wallis test
[13]
Pearson correlation coefficient
[14]
Spearman rank correlation coefficient
[15]
Kaplan-Meier curves with log-rank test
decisive
false
statistical_method object · 3 fields
minimax
Kaplan-Meier curves with the log-rank test
minimax_alt
Kaplan-Meier curves with the log-rank test for survival outcomes between groups
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
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null
evidence
null
[3] object · 4 fields
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protocol_reconstruction
status
pending
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null
evidence
null
[4] object · 4 fields
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control_execution
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pending
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null
evidence
null
[5] object · 4 fields
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control_comparison
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pending
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null
evidence
null
[6] object · 4 fields
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publication
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pending
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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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execution.not_run
provenance object · 7 fields
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[0] object · 3 fields
id
package:993dd04c57f88e3cb9709dcadd40f79768eab5002c216502c7c5b82bf58dcea1
type
sep_package
label
SEP v1 package for pmid:40760079
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40760079
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conversion
used array · 1 item
[0]
package:993dd04c57f88e3cb9709dcadd40f79768eab5002c216502c7c5b82bf58dcea1
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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
[2] object · 3 fields
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agent:corpus-assay-engine
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dsl_catalogue_fingerprint
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capability_table_fingerprint
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lineage object · 4 fields
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fork_of
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gaps array · 13 items
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abstract
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asset:source:pmid:40760079 not verified
[2]
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corpus_record_absent
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execution.not_run
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review.human_critique
[8]
review.machine_critique.blocked
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step:obtain_source_data blocked on data:not_downloaded
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step:run_analysis blocked on no owned computational capability is bound to this experiment
[11]
step:run_analysis input 'materials:the source data behind the published result in pmid:40760079' does not resolve to a declared asset
[12]
targets
Complete file
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{"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "57a838417614b8028b5745c97fa8861ac92db202420fe574529583db7710b257", "source_hash": "73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c", "raw_response_sha256": "sha256:3119a0f1431943b8d752589566a5fcefd736a4df7b9ff422a3acee4606c9b184", "raw_response_chars": 67018}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "0bfeb5a126e81271e670520b487573186e786643353194f2814234d2fee3362c", "source_hash": "73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c", "raw_response": "{\"parent_value\":432,\"unit\":\"patients\",\"evidence\":\"This study aimed to develop a chemokine-based model for predicting radiosensitivity in HNSCC using a retrospective analysis of 432 patients from the TCGA database.\",\"target_result\":\"The study analyzed 432 patients from the TCGA database.\",\"number_stated\":true}", "reading": {"parent_value": 432, "unit": "patients", "evidence": "This study aimed to develop a chemokine-based model for predicting radiosensitivity in HNSCC using a retrospective analysis of 432 patients from the TCGA database.", "target_result": "The study analyzed 432 patients from the TCGA database.", "number_stated": true, "source_locator": "chars 196-359 of source sha256 73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c"}, "recorded_at": "2026-10-31T15:28:09.288029+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "61988ab0af4f9e59f39696fd0646367a0987ca5d788a1cdca225e3d51b8f3069", "source_hash": "73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c", "raw_response": "<think>We need answer JSON only. Need identify single numerical result headline main finding. Source abstract says retrospective analysis 432 patients. Registered target \"headline numerical result paper states for its main finding.\" Likely 432 patients. Need exact contiguous quote contains number, unit printed. Evidence exact clause. parent_value 432, unit \"patients\". target_result perhaps \"432 patients\". Need ensure whether headline result could be cohort size or p&lt;0.05? Main finding numerical result perhaps 432 patients from TCGA. Prompt specifically asks \"single numerical result that a replication of registered target has to reproduce\" and registered target main finding. Given supplied text only abstract and methods; only salient result number is 432 patients. The target likely numerical result perhaps cohort size. Evidence exact quotation: \"This study aimed to develop a chemokine-based model for predicting radiosensitivity in HNSCC using a retrospective analysis of 432 patients from the TCGA database.\" Unit \"patients\". number_stated true. target_result could state \"The model was developed using a retrospective analysis of 432 patients from the TCGA database.\" But perhaps exact source. Need output JSON valid. Ensure evidence whole clause for attribution. Exact quote. Headline number only perhaps target_result should just be \"432 patients\"? They said report headline number only; schema includes target_result. We can say \"432 patients\". Evidence full clause. Parent value 432, unit patients.</think>\n\n{\"parent_value\":432,\"unit\":\"patients\",\"evidence\":\"This study aimed to develop a chemokine-based model for predicting radiosensitivity in HNSCC using a retrospective analysis of 432 patients from the TCGA database.\",\"target_result\":\"432 patients\",\"number_stated\":true}", "reading": {"parent_value": 432, "unit": "patients", "evidence": "This study aimed to develop a chemokine-based model for predicting radiosensitivity in HNSCC using a retrospective analysis of 432 patients from the TCGA database.", "target_result": "432 patients", "number_stated": true, "source_locator": "chars 196-359 of source sha256 73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c"}, "recorded_at": "2026-10-31T15:28:10.297345+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "In a retrospective analysis of 432 HNSCC patients, a model incorporating CXCL2, CCL28, and CCR8 expression stratified patients into radiosensitive and radioresistant groups; the radiosensitive group showed significantly improved overall survival with radiotherapy.", "minimax_alt": "unclear: the supplied text reports a retrospective analysis of 432 patients from the TCGA database and a CXCL2/CCL28/CCR8 model that stratified patients into radiosensitive and radioresistant groups, with significantly improved overall survival in the radiosensitive group receiving radiotherapy; no numerical effect estimate, group-specific count, hazard ratio, target-specific p value, or model-performance metric is reported for the headline finding.", "decisive": false}, "physical_methods": {"minimax": ["In vitro experiments using radiosensitive and radioresistant tongue squamous cell carcinoma cell lines"], "minimax_alt": ["In vitro experiments using radiosensitive and radioresistant Tongue squamous cell carcinoma (TSCC) cell lines"], "decisive": false}, "analysis_methods": {"minimax": ["ESTIMATE algorithm", "Single-sample Gene Set Enrichment Analysis (ssGSEA)", "CIBERSORT algorithm", "Gene Set Variation Analysis (GSVA)", "Gene Ontology analysis", "Tumor Immune Dysfunction and Exclusion (TIDE) score", "Immunophenotype Scores (IPS)", "pRRophetic R package", "Chi-square test", "Mann-Whitney U test", "Kruskal-Wallis test", "Pearson correlation coefficient", "Spearman rank correlation coefficient", "Kaplan-Meier curves", "Log-rank test"], "minimax_alt": ["Retrospective analysis of 432 patients from the TCGA database", "Chemokine-based radiosensitivity model incorporating CXCL2, CCL28, and CCR8 expression", "ESTIMATE algorithm", "Single-sample Gene Set Enrichment Analysis (ssGSEA)", "CIBERSORT", "Gene Set Variation Analysis (GSVA) for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment", "Gene Ontology (GO) analysis", "Tumor Immune Dysfunction and Exclusion (TIDE) score", "Immunophenotype Scores (IPS) for CTLA-4 and PD-1 blockade", "pRRophetic R package with Genomics of Drug Sensitivity in Cancer (GDSC) data", "Chi-square test", "Mann-Whitney U test", "Kruskal-Wallis test", "Pearson correlation coefficient", "Spearman rank correlation coefficient", "Kaplan-Meier curves with log-rank test"], "decisive": false}, "statistical_method": {"minimax": "Kaplan-Meier curves with the log-rank test", "minimax_alt": "Kaplan-Meier curves with the log-rank test for survival outcomes between groups", "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:993dd04c57f88e3cb9709dcadd40f79768eab5002c216502c7c5b82bf58dcea1", "type": "sep_package", "label": "SEP v1 package for pmid:40760079"}], "activities": [{"id": "activity:conversion:pmid:40760079", "type": "conversion", "used": ["package:993dd04c57f88e3cb9709dcadd40f79768eab5002c216502c7c5b82bf58dcea1"], "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": "44388023-53a0-4a2d-b8da-e4ba3fd1527a", "parent_hash": "993dd04c57f88e3cb9709dcadd40f79768eab5002c216502c7c5b82bf58dcea1", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40760079 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:40760079' does not resolve to a declared asset", "targets"]}