Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:41356822

Prognostic value of the Geriatric Nutritional Risk Index in sepsis-associated acute kidney injury: a retrospective cohort study.

Guangqin Ren · Huali Tang · Xue Guo · Yunxue He · Zhengrong Ding · Zhiwei Li · Cong Zhou · Bin Li · Huibing Chen · Lijuan Dong

Frontiers in nutrition · 2025 doi:10.3389/fnut.2025.1635568

Paper

complete

Experiment

partial

Data

partial

Analysis

partial

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:41356822
kind
science-record
content_hash
sha256:6619394b7e24e4d4253e613c93cf3e4645301eba2afcacfca0b4d4ce34a3c4fd
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:31:22Z
updated_at
2026-11-01T22:15:08Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Prognostic value of the Geriatric Nutritional Risk Index in sepsis-associated acute kidney injury: a retrospective cohort study.
doi
10.3389/fnut.2025.1635568
pmid
41356822
authors array · 10 items
[0]
Guangqin Ren
[1]
Huali Tang
[2]
Xue Guo
[3]
Yunxue He
[4]
Zhengrong Ding
[5]
Zhiwei Li
[6]
Cong Zhou
[7]
Bin Li
[8]
Huibing Chen
[9]
Lijuan Dong
journal
Frontiers in nutrition
year
2025
abstract
Background: The Geriatric Nutritional Risk Index (GNRI) is a simple and objective tool for assessing nutritional status. It has shown prognostic value in patients with acute kidney injury (AKI). However, evidence in sepsis-associated AKI (S-AKI) remains limited, especially among patients receiving continuous renal replacement therapy (CRRT). Methods: This retrospective cohort study included 773 critically ill S-AKI patients who received CRRT, using data from the publicly available Dryad database. Patients were stratified into tertiles based on GNRI values. Cox proportional hazards models were employed to assess the association between GNRI and 28-day and 90-day all-cause mortality, with the lowest tertile serving as the reference group. Kaplan-Meier survival analyses were used to compare cumulative mortality across GNRI strata. Results: Among 773 patients, the 28-day and 90-day mortality rates were 61.7% and 73.0%, respectively. After adjusting for multiple confounders, higher GNRI scores were independently associated with lower all-cause mortality. Compared to the lowest GNRI group, the highest tertile showed significantly reduced mortality risks (28-day HR = 0.53; 95% CI: 0.47-0.75; p < 0.001; 90-day HR = 0.50; 95% CI: 0.41-0.63; p < 0.001). The association remained robust in subgroup analyses and was particularly pronounced in patients aged ≥65 years. Conclusion: GNRI independently predicts short-term mortality in critically ill S-AKI patients on CRRT. It is simple, objective, and integrates nutritional and inflammatory status. It can assist early risk stratification and nutritional assessment.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Cox proportional hazards regression models were used to evaluate the association between GNRI and mortality.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41356822
locator
sections[7] "Statistical analysis" paragraph 2
quote
Cox proportional hazards regression models were used to evaluate the association between GNRI and mortality.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The original contributions presented in this study are included in this article/Supplementary material, further inquiries can be directed to the corresponding authors.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41356822
locator
sections[18] "Data availability statement" paragraph 2
quote
The original contributions presented in this study are included in this article/Supplementary material, further inquiries can be directed to the corresponding authors.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
Compared to the lowest GNRI group, the highest tertile showed significantly reduced mortality risks (28-day HR = 0.53; 95% CI: 0.47–0.75; p < 0.001; 90-day HR = 0.50; 95% CI: 0.41–0.63; p < 0.001).
kind
quantitative
target object · 4 fields
value
95
unit
per cent
tolerance
null
source
Compared to the lowest GNRI group, the highest tertile showed significantly reduced mortality risks (28-day HR = 0.53; 95% CI: 0.47–0.75; p < 0.001; 90-day HR = 0.50; 95% CI: 0.41–0.63; p < 0.001).
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41356822
locator
sections[0] "Abstract" paragraph 3
quote
Compared to the lowest GNRI group, the highest tertile showed significantly reduced mortality risks (28-day HR = 0.53; 95% CI: 0.47–0.75; p < 0.001; 90-day HR = 0.50; 95% CI: 0.41–0.63; p < 0.001).
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
Compared to the lowest GNRI group, the highest tertile showed significantly reduced mortality risks (28-day HR = 0.53; 95% CI: 0.47–0.75; p < 0.001; 90-day HR = 0.50; 95% CI: 0.41–0.63; p < 0.001).
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate from the source
kind
other
state
complete
blocked_on
null
description
The claim, method and evidence span published with the source article.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:41356822
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data from the named repository
kind
data-preparation
state
blocked
blocked_on
data:accession_absent
description
The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the published analysis
kind
analysis
state
complete
blocked_on
null
description
Apply the paper's statistical method to the resolved series and compare the result with the published target.
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the replicated result and its comparison
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 · 1 item
[0]
step:obtain_source_data blocked on data:accession_absent
data object · 3 fields
state
partial
assets array · 1 item
[0] object · 15 fields
id
source:pmid:41356822
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3389/fnut.2025.1635568
sha256
sha256:8590402a5f98c73e6f3c52d2b07d801c6d4661defa0e673a0a9e1a381731ce86
bytes
25539
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3389/fnut.2025.1635568
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC12678099
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
gaps array · 0 items
analysis object · 4 fields
state
partial
methods array · 5 items
[0] object · 10 fields
id
method-1
family
survival_analysis
specific
cox_proportional_hazards
label
Survival analysis
dsl_operations array · 1 item
[0]
cox_ph
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
1
band
verbatim
quote
Cox proportional hazards regression models were used to evaluate the association between GNRI and mortality.
[1] object · 10 fields
id
method-2
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
0.8
band
high
quote
ANOVA
[2] object · 10 fields
id
method-3
family
survival_analysis
specific
kaplan_meier
label
Survival analysis
dsl_operations array · 1 item
[0]
survival_km
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.7
band
medium
quote
Kaplan-Meier
[3] object · 10 fields
id
method-4
family
survival_analysis
specific
log_rank_test
label
Survival analysis
dsl_operations array · 1 item
[0]
logrank_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.8
band
high
quote
log-rank
[4] object · 10 fields
id
method-5
family
contingency_analysis
specific
chi_square
label
Categorical (contingency table) analysis
dsl_operations array · 1 item
[0]
chi_square_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
categorical_cross_tabulation
evidence object · 3 fields
score
0.8
band
high
quote
chi-square
targets array · 2 items
[0] object · 8 fields
id
target-published-estimate
claim_id
claim-target-result
operation
bootstrap_mean_difference
unit
per cent
tolerance
null
state
complete
note
The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none.
[1] object · 8 fields
id
target-published-estimate-p-value
claim_id
claim-target-result
operation
bootstrap_mean_difference
unit
p-value
tolerance
null
state
complete
note
The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold.
gaps array · 1 item
[0]
method.reader_differs_from_extractor
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
blocked
tier
R4
blocked_on
data:accession_absent
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 1 item
[0]
cox_ph
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R4
reachable
false
accessions array · 0 items
resolved_accessions array · 0 items
statements array · 1 item
[0]
The original contributions presented in this study are included in this article/Supplementary material, further inquiries can be directed to the corresponding authors.
basis
The paper names no accession to its source data, so the data has to come from the authors.
can_run object · 3 fields
dsl_operations array · 1 item
[0]
cox_ph
assets array · 1 item
[0]
source:pmid:41356822
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:None
gaps array · 1 item
[0]
data:accession_absent
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-11-01T20:07:26Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
7664
completion_tokens
1382
cached_tokens
256
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:41356822
type
paper
label
pmid:41356822
[1] object · 3 fields
id
source:pmid:41356822
type
manuscript
label
PMID 41356822 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:41356822
type
paper
label
pmid:41356822
[1] object · 3 fields
id
source:pmid:41356822
type
manuscript
label
PMID 41356822 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-41356822
type
extraction
used array · 1 item
[0]
source:pmid:41356822
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-None
type
accession_resolution
used array · 1 item
[0]
data:geo:None
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:41356822
parent_hash
sha256:43115b4127313a29cf87e0d0e2f2f1d4be69e26de99249b195a8dcd5bacd03a5
fork_of
null
gaps array · 6 items
[0]
execution.not_run
[1]
method.reader_differs_from_extractor
[2]
review.human_critique
[3]
review.independent_reader
[4]
review.machine_critique
[5]
step:obtain_source_data blocked on data:accession_absent
assays array · 1 item
[0] object · 11 fields
role
analysis
definition_id
survival_analysis
definition_version
f2132e96ae6c7a4e
required_operations array · 1 item
[0]
cox_ph
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Cox proportional hazards regression models were used to evaluate the association between GNRI and mortality.
order_basis
analysis_only
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41356822", "kind": "science-record", "revision": 3, "content_hash": "sha256:6619394b7e24e4d4253e613c93cf3e4645301eba2afcacfca0b4d4ce34a3c4fd", "created_at": "2026-11-01T20:31:22Z", "updated_at": "2026-11-01T22:15:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic value of the Geriatric Nutritional Risk Index in sepsis-associated acute kidney injury: a retrospective cohort study.", "doi": "10.3389/fnut.2025.1635568", "pmid": "41356822", "authors": ["Guangqin Ren", "Huali Tang", "Xue Guo", "Yunxue He", "Zhengrong Ding", "Zhiwei Li", "Cong Zhou", "Bin Li", "Huibing Chen", "Lijuan Dong"], "journal": "Frontiers in nutrition", "year": 2025, "abstract": "Background: The Geriatric Nutritional Risk Index (GNRI) is a simple and objective tool for assessing nutritional status. It has shown prognostic value in patients with acute kidney injury (AKI). However, evidence in sepsis-associated AKI (S-AKI) remains limited, especially among patients receiving continuous renal replacement therapy (CRRT).\nMethods: This retrospective cohort study included 773 critically ill S-AKI patients who received CRRT, using data from the publicly available Dryad database. Patients were stratified into tertiles based on GNRI values. Cox proportional hazards models were employed to assess the association between GNRI and 28-day and 90-day all-cause mortality, with the lowest tertile serving as the reference group. Kaplan-Meier survival analyses were used to compare cumulative mortality across GNRI strata.\nResults: Among 773 patients, the 28-day and 90-day mortality rates were 61.7% and 73.0%, respectively. After adjusting for multiple confounders, higher GNRI scores were independently associated with lower all-cause mortality. Compared to the lowest GNRI group, the highest tertile showed significantly reduced mortality risks (28-day HR = 0.53; 95% CI: 0.47-0.75; p < 0.001; 90-day HR = 0.50; 95% CI: 0.41-0.63; p < 0.001). The association remained robust in subgroup analyses and was particularly pronounced in patients aged ≥65 years.\nConclusion: GNRI independently predicts short-term mortality in critically ill S-AKI patients on CRRT. It is simple, objective, and integrates nutritional and inflammatory status. It can assist early risk stratification and nutritional assessment.", "claims": [{"id": "claim-method", "statement": "Cox proportional hazards regression models were used to evaluate the association between GNRI and mortality.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41356822", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Cox proportional hazards regression models were used to evaluate the association between GNRI and mortality."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in this study are included in this article/Supplementary material, further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41356822", "locator": "sections[18] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in this study are included in this article/Supplementary material, further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Compared to the lowest GNRI group, the highest tertile showed significantly reduced mortality risks (28-day HR = 0.53; 95% CI: 0.47–0.75; p < 0.001; 90-day HR = 0.50; 95% CI: 0.41–0.63; p < 0.001).", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Compared to the lowest GNRI group, the highest tertile showed significantly reduced mortality risks (28-day HR = 0.53; 95% CI: 0.47–0.75; p < 0.001; 90-day HR = 0.50; 95% CI: 0.41–0.63; p < 0.001)."}, "evidence": [{"asset": "source:pmid:41356822", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Compared to the lowest GNRI group, the highest tertile showed significantly reduced mortality risks (28-day HR = 0.53; 95% CI: 0.47–0.75; p < 0.001; 90-day HR = 0.50; 95% CI: 0.41–0.63; p < 0.001)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Compared to the lowest GNRI group, the highest tertile showed significantly reduced mortality risks (28-day HR = 0.53; 95% CI: 0.47–0.75; p < 0.001; 90-day HR = 0.50; 95% CI: 0.41–0.63; p < 0.001).", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41356822"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41356822", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fnut.2025.1635568", "sha256": "sha256:8590402a5f98c73e6f3c52d2b07d801c6d4661defa0e673a0a9e1a381731ce86", "bytes": 25539, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fnut.2025.1635568", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12678099", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Cox proportional hazards regression models were used to evaluate the association between GNRI and mortality."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-4", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-5", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 0.001, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The original contributions presented in this study are included in this article/Supplementary material, further inquiries can be directed to the corresponding authors."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:41356822"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:07:26Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 7664, "completion_tokens": 1382, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:41356822", "type": "paper", "label": "pmid:41356822"}, {"id": "source:pmid:41356822", "type": "manuscript", "label": "PMID 41356822 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41356822", "type": "paper", "label": "pmid:41356822"}, {"id": "source:pmid:41356822", "type": "manuscript", "label": "PMID 41356822 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41356822", "type": "extraction", "used": ["source:pmid:41356822"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:41356822", "parent_hash": "sha256:43115b4127313a29cf87e0d0e2f2f1d4be69e26de99249b195a8dcd5bacd03a5", "fork_of": null, "generation": 2}, "gaps": ["execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Cox proportional hazards regression models were used to evaluate the association between GNRI and mortality."], "order_basis": "analysis_only", "id": "assay:1"}]}