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pmid:40640931

MTHFD1L is a novel prognostic marker and therapeutic target in cutaneous melanoma.

Diagnostic pathology · 2025 doi:10.1186/s13000-025-01680-9

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
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pmid:40640931
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science-record
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sha256:3a485ce88bcb4e8edd61d51a7198e04969a7757659ee73ded5bb6bc0f6755a38
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https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
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2026-11-01T10:25:51Z
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2026-11-01T14:01:43Z
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corpus-assay-engine
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sep_to_sci_v1
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paper object · 10 fields
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partial
title
MTHFD1L is a novel prognostic marker and therapeutic target in cutaneous melanoma.
doi
10.1186/s13000-025-01680-9
pmid
40640931
authors
null
journal
Diagnostic pathology
year
2025
abstract
null
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the headline numerical result the paper states for its main finding
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qualitative
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null
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null
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the headline numerical result the paper states for its main finding
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Read the published estimate and its interval from the source
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other
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The number a replication must land on, and the sentence it came from.
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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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Run the analysis programme
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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:40640931
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Source read by the package builder: full_text.
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Comparisons between MTHFD1L expression level and clinical features in SKCM patients based on the TCGA-SKCM datasets
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pmcid
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section_index
23
section_title
Relationship between MTHFD1L and clinical features in SKCM patients
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Table 1
caption
Comparisons between MTHFD1L expression level and clinical features in SKCM patients based on the TCGA-SKCM datasets
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[0] array · 5 items
[0]
clinical features
[1]
n
[2]
MTHFD1L expression
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χ2
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p value
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[0]
low (n)
[1]
high (n)
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[0]
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[5]
<0.001
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Comparisons between MTHFD1L expression level and clinical features in patients with melanoma
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PMC12243374
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23
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Relationship between MTHFD1L and clinical features in SKCM patients
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Table 2
caption
Comparisons between MTHFD1L expression level and clinical features in patients with melanoma
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[0]
clinical features
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n
[2]
MTHFD1L expression
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p value
[1] array · 2 items
[0]
low (n)
[1]
high (n)
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[0]
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[2]
[3]
[4]
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[1]
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15
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[3]
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[3]
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[4]
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12
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[4]
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0
[1]
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[0]
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[1]
3
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[0]
Melanoma ulceration
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[3]
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[4]
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[27] array · 5 items
[0]
≤ 3 mm
[1]
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[2]
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[0]
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[1]
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[2]
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[3]
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[0]
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locator
section[23]/table-wrap[2]#Tab2
gaps array · 1 item
[0]
asset:source:pmid:40640931 not verified
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[0]
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[1]
targets
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null
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null
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[0]
source:pmid:40640931
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read_published_estimate
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source:pmid:40640931
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corpus_record_absent
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minimax
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{"parent_value":0,"unit":"","evidence":"","target_result":"The paper states that MTHFD1L expression was increased in SKCM tissues, high MTHFD1L expression correlated with poor overall survival, and MTHFD1L knockdown significantly inhibited proliferation, migration, invasion, and clonogenic ability in melanoma cells; no numerical result is stated for the main finding.","number_stated":false}
reading object · 6 fields
parent_value
0
unit
evidence
target_result
The paper states that MTHFD1L expression was increased in SKCM tissues, high MTHFD1L expression correlated with poor overall survival, and MTHFD1L knockdown significantly inhibited proliferation, migration, invasion, and clonogenic ability in melanoma cells; no numerical result is stated for the main finding.
number_stated
false
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null
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2026-10-31T15:19:52.819584+00:00
[1] object · 8 fields
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minimax_alt
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raw_response
<think>We need answer JSON only. Need inspect source for single numerical headline result stated for main finding registered target. Text seems abstract/results but no numerical result except sample count 340, 15 nodes, 22 immune cells, threshold 0.900, versions, datasets IDs. Headline main finding perhaps high expression poor OS, no numeric HR given. User explicitly if no number for registered target set false parent 0 unit/evidence empty target_result what text states instead. Need decide perhaps target is "headline numerical result paper states for main finding". Source doesn't give numerical value for main finding, likely no number. Need exact schema. target_result say paper states MTHFD1L levels increased and high expression correlated with poor overall survival, knockdown inhibited functions. Since evidence empty. number false. Could there be a number implicitly attached, e.g. TCGA including 340 tumor samples, but not headline result. Registered target is generic main finding; no explicit numerical result. Answer JSON. Need ensure valid JSON. target_result concise. "The paper states that MTHFD1L expression was elevated in SKCM and that high MTHFD1L expression correlated with poor overall survival, but it gives no numerical result for this main finding." Unit empty. parent 0. evidence "".</think> {"parent_value":0,"unit":"","evidence":"","target_result":"The paper states that MTHFD1L expression was elevated in SKCM and that high MTHFD1L expression correlated with poor overall survival, but it provides no numerical result for this main finding.","number_stated":false}
reading object · 6 fields
parent_value
0
unit
evidence
target_result
The paper states that MTHFD1L expression was elevated in SKCM and that high MTHFD1L expression correlated with poor overall survival, but it provides no numerical result for this main finding.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:19:55.206953+00:00
agreement
true
disagreements object · 3 fields
target_result object · 3 fields
minimax
High MTHFD1L expression correlated with poor overall survival in skin cutaneous melanoma.
minimax_alt
unclear — the supplied text gives no headline numerical result; it states only that high MTHFD1L expression correlated with poor overall survival.
decisive
false
physical_methods object · 3 fields
minimax array · 6 items
[0]
RT-qPCR
[1]
Western blot
[2]
Immunohistochemistry (IHC) staining
[3]
MTHFD1L knockdown in A375 and A2058 melanoma cells
[4]
Proliferation, migration, invasion, and clonogenic ability assays
[5]
Western blot analysis of TGF-β1, SMAD3, and phosphorylated SMAD3
minimax_alt array · 5 items
[0]
RT-qPCR
[1]
Western blot
[2]
IHC staining
[3]
Establishment of MTHFD1L knockdown models in A375 and A2058 melanoma cells
[4]
Functional characterization of proliferation, migration, invasion, and clonogenic ability
decisive
false
analysis_methods object · 3 fields
minimax array · 16 items
[0]
TCGA-SKCM and GTEx mRNA expression analysis
[1]
GSE15605 and GSE19234 gene-expression analysis
[2]
GO enrichment analysis
[3]
KEGG pathway enrichment analysis
[4]
Protein-protein interaction network construction
[5]
GEPIA2 overall-survival analysis using median MTHFD1L expression as the cutoff
[6]
Univariate Cox proportional hazards regression
[7]
Multivariate Cox proportional hazards regression
[8]
Kaplan–Meier survival analysis with log-rank tests
[9]
χ2 test
[10]
Fisher's exact test
[11]
Unpaired t-test
[12]
Two-way analysis of variance (ANOVA)
[13]
CIBERSORT immune-cell infiltration analysis
[14]
xCell immune-cell infiltration analysis
[15]
Spearman correlation analysis
minimax_alt array · 14 items
[0]
TCGA-SKCM and combined GSE15605/GSE19234 analysis of MTHFD1L mRNA expression
[1]
GEPIA2 prognostic analysis
[2]
GO enrichment analysis
[3]
KEGG pathway enrichment analysis
[4]
STRING protein-protein interaction network construction
[5]
CIBERSORT immune-cell infiltration analysis
[6]
xCell immune-cell infiltration analysis
[7]
Kaplan–Meier method with log-rank tests
[8]
Univariate and multivariate Cox proportional hazard regression
[9]
χ2 test
[10]
Fisher’s exact test
[11]
Unpaired t-test
[12]
Two-way analysis of variance (ANOVA)
[13]
Spearman correlation analysis
decisive
false
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
status
pending
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null
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null
[1] object · 4 fields
key
independent_readings
status
passed
reason
The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
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key
source_resolution
status
pending
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null
evidence
null
[3] object · 4 fields
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status
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null
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null
[4] object · 4 fields
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null
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null
[5] object · 4 fields
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null
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null
[6] object · 4 fields
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agent:minimax
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agent:minimax_alt
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minimax_alt
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abstract
[1]
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step:obtain_source_data blocked on data:not_downloaded
[10]
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:40640931' does not resolve to a declared asset
[12]
targets
Complete file
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"40", "20", "20", "", ""], ["Metastasis", "", "", "", "2.349", "0.125"], ["M0", "329", "167", "162", "", ""], ["M1", "11", "3", "8", "", ""]], "row_count": 21, "column_count": 6, "numeric_cells": 54, "header_rows": 2, "locator": "section[23]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:40640931:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:50026e09b1c8fe0e44e653b59035aab5a2d08ecf93a655cd9426425df2ca466b", "bytes": 1117, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[2]#Tab2", "version": null, "note": "Comparisons between MTHFD1L expression level and clinical features in patients with melanoma", "structure": {"pmcid": "PMC12243374", "section_index": 23, "section_title": "Relationship between MTHFD1L and clinical features in SKCM patients", "row_count": 32, "column_count": 5}, "table": {"label": "Table 2", "caption": "Comparisons between MTHFD1L expression level and clinical features in patients with melanoma", "rows": [["clinical features", "n", "MTHFD1L expression", "p value"], ["low (n)", "high (n)"], ["Gender", "", "", "", "0.21"], ["Male", "12", "5", "7", ""], ["Female", "18", "3", "15"], ["Age (years)", "", "", "", "1"], ["≤ 55", "9", "2", "7", ""], [">55", "21", "6", "15"], ["Clinical stage", "", "", "", "0.417"], ["I&II", "19", "4", "15", ""], ["III&IV", "11", "4", "7"], ["T stage", "", "", "", "0.672"], ["1&2", "11", "2", "9", ""], ["3&4", "19", "6", "13"], ["N stage", "", "", "", "0.699"], ["0", "18", "5", "13", ""], ["1&2&3", "12", "3", "9"], ["Metastasis", "", "", "", "1"], ["0", "27", "7", "20", ""], ["1", "3", "1", "2"], ["Melanoma ulceration", "", "", "", "0.007"], ["no", "7", "5", "2", ""], ["yes", "23", "3", "20"], ["Clark level", "", "", "", "0.028"], ["I&II&III", "11", "6", "5", ""], ["IV&V", "19", "2", "17"], ["Breslow depth", "", "", "", "0.407"], ["≤ 3 mm", "13", "2", "11", ""], [">3 mm", "17", "6", "11"], ["Chemotherapy", "", "", "", "1"], ["no", "17", "5", "12", ""], ["yes", "13", "3", "10"]], "row_count": 32, "column_count": 5, "numeric_cells": 80, "header_rows": 2, "locator": "section[23]/table-wrap[2]#Tab2"}}], "gaps": ["asset:source:pmid:40640931 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:40640931", "asset:table:pmid:40640931:1", "asset:table:pmid:40640931:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40640931"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "passed", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "6026320114fab6ee7d189f8e5848b0f01676193fbe08cc13b49805ff6a1839bd", "source_hash": "e8bcccc78ba07f9beab001dd8ee5fe95c3910429887bbdb31d33d6468b17e5c0", "raw_response_sha256": "sha256:ba3f973082d0d75da4eecb2b9f10af8766e5e014c94b271a28e0307e60c220e7", "raw_response_chars": 8026}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "dc6e40d16dbb4d9aed47059e3911a66a9dcbd7fa22a39388f2f3bcb36c8ecde2", "source_hash": "e8bcccc78ba07f9beab001dd8ee5fe95c3910429887bbdb31d33d6468b17e5c0", "raw_response_sha256": "sha256:451d103f21021aabd75b7e391c978833e350384edaeb00d02b5d0db825af0c52", "raw_response_chars": 68034}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "ec4ae7af78eeec2d18831e960b28ad0ec07e409b69c78c2dc43feb875b9c825f", "source_hash": "e8bcccc78ba07f9beab001dd8ee5fe95c3910429887bbdb31d33d6468b17e5c0", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that MTHFD1L expression was increased in SKCM tissues, high MTHFD1L expression correlated with poor overall survival, and MTHFD1L knockdown significantly inhibited proliferation, migration, invasion, and clonogenic ability in melanoma cells; no numerical result is stated for the main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that MTHFD1L expression was increased in SKCM tissues, high MTHFD1L expression correlated with poor overall survival, and MTHFD1L knockdown significantly inhibited proliferation, migration, invasion, and clonogenic ability in melanoma cells; no numerical result is stated for the main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:19:52.819584+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "c0c70517422ef012559b13cc0153b3a5b035c3254efa864d9886e4b6203660b3", "source_hash": "e8bcccc78ba07f9beab001dd8ee5fe95c3910429887bbdb31d33d6468b17e5c0", "raw_response": "<think>We need answer JSON only. Need inspect source for single numerical headline result stated for main finding registered target. Text seems abstract/results but no numerical result except sample count 340, 15 nodes, 22 immune cells, threshold 0.900, versions, datasets IDs. Headline main finding perhaps high expression poor OS, no numeric HR given. User explicitly if no number for registered target set false parent 0 unit/evidence empty target_result what text states instead. Need decide perhaps target is \"headline numerical result paper states for main finding\". Source doesn't give numerical value for main finding, likely no number. Need exact schema. target_result say paper states MTHFD1L levels increased and high expression correlated with poor overall survival, knockdown inhibited functions. Since evidence empty. number false. Could there be a number implicitly attached, e.g. TCGA including 340 tumor samples, but not headline result. Registered target is generic main finding; no explicit numerical result. Answer JSON.\n\nNeed ensure valid JSON. target_result concise. \"The paper states that MTHFD1L expression was elevated in SKCM and that high MTHFD1L expression correlated with poor overall survival, but it gives no numerical result for this main finding.\" Unit empty. parent 0. evidence \"\".</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that MTHFD1L expression was elevated in SKCM and that high MTHFD1L expression correlated with poor overall survival, but it provides no numerical result for this main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that MTHFD1L expression was elevated in SKCM and that high MTHFD1L expression correlated with poor overall survival, but it provides no numerical result for this main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:19:55.206953+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "High MTHFD1L expression correlated with poor overall survival in skin cutaneous melanoma.", "minimax_alt": "unclear — the supplied text gives no headline numerical result; it states only that high MTHFD1L expression correlated with poor overall survival.", "decisive": false}, "physical_methods": {"minimax": ["RT-qPCR", "Western blot", "Immunohistochemistry (IHC) staining", "MTHFD1L knockdown in A375 and A2058 melanoma cells", "Proliferation, migration, invasion, and clonogenic ability assays", "Western blot analysis of TGF-β1, SMAD3, and phosphorylated SMAD3"], "minimax_alt": ["RT-qPCR", "Western blot", "IHC staining", "Establishment of MTHFD1L knockdown models in A375 and A2058 melanoma cells", "Functional characterization of proliferation, migration, invasion, and clonogenic ability"], "decisive": false}, "analysis_methods": {"minimax": ["TCGA-SKCM and GTEx mRNA expression analysis", "GSE15605 and GSE19234 gene-expression analysis", "GO enrichment analysis", "KEGG pathway enrichment analysis", "Protein-protein interaction network construction", "GEPIA2 overall-survival analysis using median MTHFD1L expression as the cutoff", "Univariate Cox proportional hazards regression", "Multivariate Cox proportional hazards regression", "Kaplan–Meier survival analysis with log-rank tests", "χ2 test", "Fisher's exact test", "Unpaired t-test", "Two-way analysis of variance (ANOVA)", "CIBERSORT immune-cell infiltration analysis", "xCell immune-cell infiltration analysis", "Spearman correlation analysis"], "minimax_alt": ["TCGA-SKCM and combined GSE15605/GSE19234 analysis of MTHFD1L mRNA expression", "GEPIA2 prognostic analysis", "GO enrichment analysis", "KEGG pathway enrichment analysis", "STRING protein-protein interaction network construction", "CIBERSORT immune-cell infiltration analysis", "xCell immune-cell infiltration analysis", "Kaplan–Meier method with log-rank tests", "Univariate and multivariate Cox proportional hazard regression", "χ2 test", "Fisher’s exact test", "Unpaired t-test", "Two-way analysis of variance (ANOVA)", "Spearman correlation analysis"], "decisive": false}}, "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": "passed", "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.passed"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:158fc3f51d55993d35037424f669feb7a2dd8cded70a16637de334d3e957c0c8", "type": "sep_package", "label": "SEP v1 package for pmid:40640931"}], "activities": [{"id": "activity:conversion:pmid:40640931", "type": "conversion", "used": ["package:158fc3f51d55993d35037424f669feb7a2dd8cded70a16637de334d3e957c0c8"], "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:40640931", "parent_hash": "sha256:d64a4a0ea524b8c164140be48b1e05ced95da8ff9818eb14e2c8bd7de6ff5ff1", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40640931 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.passed", "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:40640931' does not resolve to a declared asset", "targets"]}