← All .science files
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
generator object · 3 fields
paper object · 10 fields
claims array · 1 item
[0] object · 6 fields
target object · 4 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 2 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
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
data object · 3 fields
assets array · 1 item
[0] object · 15 fields
structure object · 1 field
gaps array · 1 item
capability object · 3 fields
readiness object · 8 fields
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 1 item
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 7 fields
providers array · 2 items
[0] object · 7 fields
[1] object · 7 fields
target_providers array · 2 items
[0] object · 8 fields
reading object · 6 fields
[1] object · 8 fields
reading object · 6 fields
disagreements object · 4 fields
target_result object · 3 fields
physical_methods object · 3 fields
minimax array · 1 item
minimax_alt array · 1 item
analysis_methods object · 3 fields
minimax array · 15 items
minimax_alt array · 16 items
statistical_method object · 3 fields
agreement_basis object · 2 fields
decisive_fields array · 4 items
human_critique object · 5 fields
stages array · 7 items
[0] object · 4 fields
[1] object · 4 fields
evidence object · 1 field
provider_errors array · 0 items
[2] object · 4 fields
[3] object · 4 fields
[4] object · 4 fields
[5] object · 4 fields
[6] object · 4 fields
gaps array · 2 items
provenance object · 7 fields
entities array · 1 item
activities array · 1 item
agents array · 3 items
lineage object · 4 fields
gaps array · 13 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40760079", "kind": "science-record", "revision": 1, "content_hash": "sha256:8e0b4b85e2ffb3f97be946d9b776858db1c92b2c40dc81c30c025f55222e6cae", "created_at": "2026-11-01T10:25:52Z", "updated_at": "2026-11-01T10:25:52Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"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": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 432.0, "unit": "patients", "tolerance": null, "source": "chars 196-359 of source sha256 73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c"}, "evidence": [{"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": ["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:40760079"], "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:40760079", "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:40760079' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40760079", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-13346-z", "sha256": "sha256:73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-13346-z", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:40760079 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:40760079"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40760079"]}, "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": "a6a66955d743436c84ba69efd3275fb6c1a3fcf1d74394cde004630b74a0b4b5", "source_hash": "73d1ebee23ece4c8aa00440676057171bebd05cd978764434a3d6cc12db9833c", "raw_response_sha256": "sha256:c0f67a213e88950e137336d03653f5ee6fe76ccbf5ddf208f857eda46418aa4d", "raw_response_chars": 5782}, {"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<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"]}