← All .science files
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
generator object · 3 fields
paper object · 10 fields
claims array · 1 item
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 · 5 items
minimax_alt array · 5 items
analysis_methods object · 3 fields
minimax array · 12 items
minimax_alt array · 11 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:41483244", "kind": "science-record", "revision": 1, "content_hash": "sha256:731e0d88d44169cb09a6c9ff4a893ed6be4670452848a5aafba56bc17e2fd345", "created_at": "2026-11-01T10:25:54Z", "updated_at": "2026-11-01T10:25:54Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"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": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41483244"], "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:41483244", "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:41483244' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41483244", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s10238-025-02026-x", "sha256": "sha256:ab98f46775d6d737a15cce3c05ef40d2ef9231ccda2c648cc14d8e3bfeda704b", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s10238-025-02026-x", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:41483244 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:41483244"], "steps": ["read_published_estimate"]}, "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 > 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"]}