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pmid:41483244

Bioinformatics and experimental approaches identify NME8 as a promoter of the metastasis of renal cell carcinoma by activating the JAK/STAT signaling pathway.

Clinical and experimental medicine · 2026 doi:10.1007/s10238-025-02026-x

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:41483244
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science-record
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sha256:731e0d88d44169cb09a6c9ff4a893ed6be4670452848a5aafba56bc17e2fd345
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https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
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2026-11-01T10:25:54Z
updated_at
2026-11-01T10:25:54Z
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
Bioinformatics and experimental approaches identify NME8 as a promoter of the metastasis of renal cell carcinoma by activating the JAK/STAT signaling pathway.
doi
10.1007/s10238-025-02026-x
pmid
41483244
authors
null
journal
Clinical and experimental medicine
year
2026
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
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qualitative
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blocked
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null
unit
null
tolerance
null
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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.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:41483244
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
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obtain_source_data
order
2
name
Obtain the source data behind the published result
kind
data-preparation
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blocked
blocked_on
data:not_downloaded
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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
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run_analysis
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3
name
Run the analysis programme
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analysis
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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:41483244
parameters object · 0 fields
inputs array · 0 items
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[0]
the registered result
instruments array · 0 items
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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
[2]
step:run_analysis input 'materials:the source data behind the published result in pmid:41483244' 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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source:pmid:41483244
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xml
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application/xml
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https://doi.org/10.1007/s10238-025-02026-x
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resolved
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null
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reader_required
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10.1007/s10238-025-02026-x
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null
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Source read by the package builder: full_text.
structure object · 1 field
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full_text
gaps array · 1 item
[0]
asset:source:pmid:41483244 not verified
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targets
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null
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source:pmid:41483244
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read_published_estimate
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xml
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source:pmid:41483244
gaps array · 1 item
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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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{"parent_value":0,"unit":"","evidence":"","target_result":"The paper states that NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, and that NME8 knockdown significantly reduced renal cancer cell proliferation, migration, and invasion while increasing apoptosis.","number_stated":false}
reading object · 6 fields
parent_value
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unit
evidence
target_result
The paper states that NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, and that NME8 knockdown significantly reduced renal cancer cell proliferation, migration, and invasion while increasing apoptosis.
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false
source_locator
null
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2026-10-31T15:27:28.317365+00:00
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minimax_alt
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raw_response
<think>We need answer JSON only. Need parse request. Need find single numerical result headline stated main finding. Source appears abstract/methods snippets, no obvious headline numerical result. Need determine if text states any number for registered target. They specifically ask value paper states for registered target, exact contiguous quote. The source has numbers but mostly methodological/software, no headline numerical result for NME8's main finding. Could perhaps target is "headline numerical result" and there is no number in supplied text. Must set number_stated false, parent_value 0, unit/evidence empty, target_result say what text states instead. Need exact JSON. We need mention qualitative findings, perhaps "NME8 is overexpressed in renal cancer..." But source doesn't give numerical result. We should not quote evidence? Empty. target_result likely "The text states that NME8 is overexpressed..." Need concise. Must ensure number isn't hidden perhaps DOI 10.1007... irrelevant, GSE66272 contains digits, P &gt; 0.05, α 0.05, cell aliquots etc. No main finding value. Maybe "main finding" could have result in abstract: NME8 knockdown significantly reduced proliferation, migration, invasion while increasing apoptosis, no values. So false. Need ensure exact schema and valid JSON. target_result could state "The text reports qualitative findings that NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, and that NME8 knockdown reduced proliferation, migration, and invasion while increasing apoptosis; it gives no headline numerical value for the main finding." This paraphrases source but target_result allowed what text states instead. No evidence since false, empty. Let's answer.</think> {"parent_value":0,"unit":"","evidence":"","target_result":"The text states that NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, and that NME8 knockdown reduced renal cancer cell proliferation, migration, and invasion while increasing apoptosis. It gives no numerical value for the main finding.","number_stated":false}
reading object · 6 fields
parent_value
0
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The text states that NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, and that NME8 knockdown reduced renal cancer cell proliferation, migration, and invasion while increasing apoptosis. It gives no numerical value for the main finding.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:27:30.927039+00:00
agreement
false
disagreements object · 4 fields
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minimax
No headline numerical result is stated in the supplied text. The main reported findings are that NME8 is overexpressed in renal cancer and is correlated with poor patient outcomes, and that NME8 promotes RCC metastasis through JAK/STAT signaling.
minimax_alt
unclear — the supplied text states no headline numerical result for the main finding. The closest stated prognosis result is qualitative: NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, as determined by Cox regression.
decisive
false
physical_methods object · 3 fields
minimax array · 5 items
[0]
Creation of stable NME8-knockdown cell lines
[1]
Cell proliferation, migration, invasion, and apoptosis assays
[2]
Flow cytometric cell-cycle analysis using Annexin V and allophycocyanin/phytoerythrin staining
[3]
Immunoblotting for EMT-associated proteins
[4]
Exposure to the JAK inhibitor ruxolitinib and the STAT3 inhibitor stattic
minimax_alt array · 5 items
[0]
Creation of stable NME8-knockdown cell lines
[1]
Renal cancer cell proliferation, migration, invasion, and apoptosis assessments
[2]
Flow-cytometric cell-cycle analysis and Annexin V apoptosis analysis
[3]
Immunoblotting of EMT-associated proteins, including E-cadherin, vimentin, and Twist
[4]
Pharmacological inhibition of JAK with ruxolitinib and STAT3 with stattic
decisive
false
analysis_methods object · 3 fields
minimax array · 12 items
[0]
Univariate and multivariate Cox proportional hazard models
[1]
Kaplan–Meier survival estimates
[2]
Schoenfeld residual tests
[3]
Median-based dichotomization of NME8 expression
[4]
Differential expression analysis using the limma R package with empirical Bayes moderation
[5]
Gene Ontology enrichment analysis
[6]
KEGG pathway analysis
[7]
CIBERSORT immune-cell estimation
[8]
ESTIMATE algorithm
[9]
Wilcoxon rank-sum tests
[10]
Spearman correlation analysis
[11]
One-way analysis of variance
minimax_alt array · 11 items
[0]
Univariate and multivariate Cox proportional hazard models for OS
[1]
Schoenfeld residual tests for the proportional-hazards assumption
[2]
Kaplan–Meier survival estimation
[3]
Median-based dichotomization of NME8 expression
[4]
limma differential-expression analysis using a linear model framework with empirical Bayes moderation
[5]
Gene Ontology and KEGG pathway enrichment analysis
[6]
CIBERSORT immune-cell estimation
[7]
ESTIMATE scoring of tumor purity, immune score, and stromal score
[8]
Wilcoxon rank-sum tests
[9]
Spearman correlation analysis
[10]
One-way analysis of variance for experimental intergroup comparisons
decisive
false
statistical_method object · 3 fields
minimax
Cox regression for hazard-ratio estimation and Kaplan–Meier survival estimates
minimax_alt
Univariate and multivariate Cox proportional hazard models for OS
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
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true
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null
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null
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null
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target_materials
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null
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null
[1] object · 4 fields
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independent_readings
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The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 0 items
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source_resolution
status
pending
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null
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null
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null
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null
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review.human_critique
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review.machine_critique.blocked
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package:d3fa7ce527044a827b0daac84b8dcb2877de09787818256b84cb8663d7da943d
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sep_package
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[0] object · 4 fields
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package:d3fa7ce527044a827b0daac84b8dcb2877de09787818256b84cb8663d7da943d
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[1] object · 3 fields
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agent:minimax_alt
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[2] object · 3 fields
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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:41483244' does not resolve to a declared asset
[12]
targets
Complete file
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"must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41483244"]}, "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": "db704f8731a21c418401eba5a8c44ac27085d84fb1b2427a299bc3d258942f38", "source_hash": "ab98f46775d6d737a15cce3c05ef40d2ef9231ccda2c648cc14d8e3bfeda704b", "raw_response_sha256": "sha256:4dc1d36807bc4e645c5c9ccdd5102aaae79b42dd761e92bf810db4fa263fe172", "raw_response_chars": 4802}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "5bca9e91a131edc6c701835433664ef60685b2504c29b4c4f9256594c401172e", "source_hash": "ab98f46775d6d737a15cce3c05ef40d2ef9231ccda2c648cc14d8e3bfeda704b", "raw_response_sha256": "sha256:77c57ed5b003ff52d5c12b42d349a6dec62a8a263e2e548944e9cc1a8d9a9e54", "raw_response_chars": 78896}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "73ae2fbb14b4f90157f751811a94759eb1fbd0aa41cd5b453120f63ad4f28f98", "source_hash": "ab98f46775d6d737a15cce3c05ef40d2ef9231ccda2c648cc14d8e3bfeda704b", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, and that NME8 knockdown significantly reduced renal cancer cell proliferation, migration, and invasion while increasing apoptosis.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, and that NME8 knockdown significantly reduced renal cancer cell proliferation, migration, and invasion while increasing apoptosis.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:27:28.317365+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "3bfb00edf1ffddadcaf038a5a1ea6e4f714a26c99f99a09c308c40733249b1ef", "source_hash": "ab98f46775d6d737a15cce3c05ef40d2ef9231ccda2c648cc14d8e3bfeda704b", "raw_response": "<think>We need answer JSON only. Need parse request. Need find single numerical result headline stated main finding. Source appears abstract/methods snippets, no obvious headline numerical result. Need determine if text states any number for registered target. They specifically ask value paper states for registered target, exact contiguous quote. The source has numbers but mostly methodological/software, no headline numerical result for NME8's main finding. Could perhaps target is \"headline numerical result\" and there is no number in supplied text. Must set number_stated false, parent_value 0, unit/evidence empty, target_result say what text states instead. Need exact JSON. We need mention qualitative findings, perhaps \"NME8 is overexpressed in renal cancer...\" But source doesn't give numerical result. We should not quote evidence? Empty. target_result likely \"The text states that NME8 is overexpressed...\" Need concise. Must ensure number isn't hidden perhaps DOI 10.1007... irrelevant, GSE66272 contains digits, P &gt; 0.05, α 0.05, cell aliquots etc. No main finding value. Maybe \"main finding\" could have result in abstract: NME8 knockdown significantly reduced proliferation, migration, invasion while increasing apoptosis, no values. So false.\n\nNeed ensure exact schema and valid JSON. target_result could state \"The text reports qualitative findings that NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, and that NME8 knockdown reduced proliferation, migration, and invasion while increasing apoptosis; it gives no headline numerical value for the main finding.\" This paraphrases source but target_result allowed what text states instead. No evidence since false, empty. Let's answer.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states that NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, and that NME8 knockdown reduced renal cancer cell proliferation, migration, and invasion while increasing apoptosis. It gives no numerical value for the main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The text states that NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, and that NME8 knockdown reduced renal cancer cell proliferation, migration, and invasion while increasing apoptosis. It gives no numerical value for the main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:27:30.927039+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "No headline numerical result is stated in the supplied text. The main reported findings are that NME8 is overexpressed in renal cancer and is correlated with poor patient outcomes, and that NME8 promotes RCC metastasis through JAK/STAT signaling.", "minimax_alt": "unclear — the supplied text states no headline numerical result for the main finding. The closest stated prognosis result is qualitative: NME8 is overexpressed in renal cancer and correlated with poor patient outcomes, as determined by Cox regression.", "decisive": false}, "physical_methods": {"minimax": ["Creation of stable NME8-knockdown cell lines", "Cell proliferation, migration, invasion, and apoptosis assays", "Flow cytometric cell-cycle analysis using Annexin V and allophycocyanin/phytoerythrin staining", "Immunoblotting for EMT-associated proteins", "Exposure to the JAK inhibitor ruxolitinib and the STAT3 inhibitor stattic"], "minimax_alt": ["Creation of stable NME8-knockdown cell lines", "Renal cancer cell proliferation, migration, invasion, and apoptosis assessments", "Flow-cytometric cell-cycle analysis and Annexin V apoptosis analysis", "Immunoblotting of EMT-associated proteins, including E-cadherin, vimentin, and Twist", "Pharmacological inhibition of JAK with ruxolitinib and STAT3 with stattic"], "decisive": false}, "analysis_methods": {"minimax": ["Univariate and multivariate Cox proportional hazard models", "Kaplan–Meier survival estimates", "Schoenfeld residual tests", "Median-based dichotomization of NME8 expression", "Differential expression analysis using the limma R package with empirical Bayes moderation", "Gene Ontology enrichment analysis", "KEGG pathway analysis", "CIBERSORT immune-cell estimation", "ESTIMATE algorithm", "Wilcoxon rank-sum tests", "Spearman correlation analysis", "One-way analysis of variance"], "minimax_alt": ["Univariate and multivariate Cox proportional hazard models for OS", "Schoenfeld residual tests for the proportional-hazards assumption", "Kaplan–Meier survival estimation", "Median-based dichotomization of NME8 expression", "limma differential-expression analysis using a linear model framework with empirical Bayes moderation", "Gene Ontology and KEGG pathway enrichment analysis", "CIBERSORT immune-cell estimation", "ESTIMATE scoring of tumor purity, immune score, and stromal score", "Wilcoxon rank-sum tests", "Spearman correlation analysis", "One-way analysis of variance for experimental intergroup comparisons"], "decisive": false}, "statistical_method": {"minimax": "Cox regression for hazard-ratio estimation and Kaplan–Meier survival estimates", "minimax_alt": "Univariate and multivariate Cox proportional hazard models for OS", "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:d3fa7ce527044a827b0daac84b8dcb2877de09787818256b84cb8663d7da943d", "type": "sep_package", "label": "SEP v1 package for pmid:41483244"}], "activities": [{"id": "activity:conversion:pmid:41483244", "type": "conversion", "used": ["package:d3fa7ce527044a827b0daac84b8dcb2877de09787818256b84cb8663d7da943d"], "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": "c4ed1794-6243-4280-9f96-55edec6e4bfc", "parent_hash": "d3fa7ce527044a827b0daac84b8dcb2877de09787818256b84cb8663d7da943d", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:41483244 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:41483244' does not resolve to a declared asset", "targets"]}