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

pmid:32935914

Diabetic nephropathy associates with deregulation of enzymes involved in kidney sulphur metabolism.

Elena Uyy · Viorel Iulian Suica · Raluca Maria Boteanu · Florentina Safciuc · Aurel Cerveanu-Hogas · Luminita Ivan · Crina Stavaru · Maya Simionescu · Felicia Antohe

Journal of cellular and molecular medicine · 2020 doi:10.1111/jcmm.15855

Paper

complete

Experiment

complete

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:32935914
kind
science-record
content_hash
sha256:615eba153f01b82de06135934bfbf7f46891fb8e2c9fee2b03039449fbbfae11
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:41:10Z
updated_at
2026-11-01T21:23:48Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Diabetic nephropathy associates with deregulation of enzymes involved in kidney sulphur metabolism.
doi
10.1111/jcmm.15855
pmid
32935914
authors array · 9 items
[0]
Elena Uyy
[1]
Viorel Iulian Suica
[2]
Raluca Maria Boteanu
[3]
Florentina Safciuc
[4]
Aurel Cerveanu-Hogas
[5]
Luminita Ivan
[6]
Crina Stavaru
[7]
Maya Simionescu
[8]
Felicia Antohe
journal
Journal of cellular and molecular medicine
year
2020
abstract
Nephropathy is a major chronic complication of diabetes. A crucial role in renal pathophysiology is played by hydrogen sulphide (H2 S) that is produced excessively by the kidney; however, the data regarding H2 S bioavailability are inconsistent. We hypothesize that early type 1 diabetes (T1D) increases H2 S production by a mechanism involving hyperglycaemia-induced alterations in sulphur metabolism. Plasma and kidney tissue collected from T1D double transgenic mice were subjected to mass spectrometry-based proteomic analysis, and the results were validated by immunological and gene expression assays.T1D mice exhibited a high concentration of H2 S in the plasma and kidney tissue and histological, showed signs of subtle kidney fibrosis, characteristic for early renal disease. The shotgun proteomic analyses disclosed that the level of enzymes implicated in sulphate activation modulators, H2 S-oxidation and H2 S-production were significantly affected (ie 6 up-regulated and 4 down-regulated). Gene expression results corroborated well with the proteomic data. Dysregulation of H2 S enzymes underly the changes occurring in H2 S production, which in turn could play a key role in the initiation of renal disease. The new findings lead to a novel target in the therapy of diabetic nephropathy. Mass spectrometry data are available via ProteomeXchange with identifier PXD018053.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
The results were analysed by Student's unpaired t test using GraphPad Prism 5.0 statistical software (GraphPad Software).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:32935914
locator
sections[11] "Statistics" paragraph 2
quote
The results were analysed by Student's unpaired t test using GraphPad Prism 5.0 statistical software (GraphPad Software).
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Data openly available in a public repository that issues datasets with DOIs.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:32935914
locator
sections[24] "DATA AVAILABILITY STATEMENT" paragraph 2
quote
Data openly available in a public repository that issues datasets with DOIs.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
null
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:32935914
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
complete
blocked_on
null
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 · 1 item
[0]
data:geo:PXD018053
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 · 1 item
[0]
data:geo:PXD018053
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 · 0 items
data object · 3 fields
state
partial
assets array · 3 items
[0] object · 15 fields
id
source:pmid:32935914
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1111/jcmm.15855
sha256
sha256:d175ee470cd063cd8d147444ec3340814a22ce57ee736da139d0ff1cdafbb623
bytes
43173
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1111/jcmm.15855
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
PMC7579703
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD018053
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD018053
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD018053
version
null
note
Data openly available in a public repository that issues datasets with DOIs.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Data openly available in a public repository that issues datasets with DOIs.
access_statement_kind
data_availability_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
Mouse early diabetic nephropathy LC-MS/MS analysis
resolution_checked_at
2026-10-31T18:35:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 16 fields
id
asset:table:pmid:32935914:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:686f38007042c821629b0c45b483d1185ffd5e85ab1750c2078cac9bc8b4f3e7
bytes
849
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[15]/table-wrap[1]#jcmm15855-tbl-0001
version
null
note
Over‐represented KEGG pathways in diabetic vs non‐diabetic kidney tissue
structure object · 5 fields
pmcid
PMC7579703
section_index
15
section_title
Modifications of kidney proteome in T1D revealed by global shotgun proteomic analysis
row_count
10
column_count
3
table object · 8 fields
label
TABLE 1
caption
Over‐represented KEGG pathways in diabetic vs non‐diabetic kidney tissue
rows array · 10 items
[0] array · 3 items
[0]
No.
[1]
Description
[2]
FDR P‐value
[1] array · 3 items
[0]
1
[1]
Sulphur metabolism (mmu00920)
[2]
3.46E‐05
[2] array · 3 items
[0]
2
[1]
Proximal tubule bicarbonate reclamation (mmu04964)
[2]
5.56E‐05
[3] array · 3 items
[0]
3
[1]
Glycine, serine and threonine metabolism (mmu00260)
[2]
6.40E‐05
[4] array · 3 items
[0]
4
[1]
Cysteine and methionine metabolism (mmu00270)
[2]
1.08E‐04
[5] array · 3 items
[0]
5
[1]
Arginine and proline metabolism (mmu00330)
[2]
3.10E‐03
[6] array · 3 items
[0]
6
[1]
D‐Glutamine and D‐glutamate metabolism (mmu00471)
[2]
3.35E‐03
[7] array · 3 items
[0]
7
[1]
Seleno‐compound metabolism (mmu00450)
[2]
5.50E‐03
[8] array · 3 items
[0]
8
[1]
Lysine degradation (mmu00310)
[2]
1.69E‐02
[9] array · 3 items
[0]
9
[1]
PPAR signalling pathway (mmu03320)
[2]
2.04E‐02
locator
section[15]/table-wrap[1]#jcmm15855-tbl-0001
gaps array · 2 items
[0]
asset:data:geo:PXD018053 not downloaded
[1]
asset:data:geo:PXD018053 licence not read
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
null
specific
null
label
Student's unpaired t test
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
The results were analysed by Student's unpaired t test using GraphPad Prism 5.0 statistical software (GraphPad Software).
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
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
blocking_axis
method
blocked_on
method:not_determinable
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (Student's unpaired t test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
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
R1
reachable
true
accessions array · 1 item
[0]
PXD018053
resolved_accessions array · 1 item
[0]
PXD018053
statements array · 1 item
[0]
Data openly available in a public repository that issues datasets with DOIs.
basis
The paper names PXD018053 in PRIDE and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 3 items
[0]
source:pmid:32935914
[1]
data:geo:PXD018053
[2]
asset:table:pmid:32935914:1
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:PXD018053
gaps array · 1 item
[0]
method:not_determinable
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
2026-10-31T18:22:29Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
33988
completion_tokens
648
cached_tokens
792
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:32935914
type
paper
label
pmid:32935914
[1] object · 3 fields
id
source:pmid:32935914
type
manuscript
label
PMID 32935914 full text
[2] object · 3 fields
id
data:geo:PXD018053
type
dataset
label
GEO PXD018053
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:32935914
type
paper
label
pmid:32935914
[1] object · 3 fields
id
source:pmid:32935914
type
manuscript
label
PMID 32935914 full text
[2] object · 3 fields
id
data:geo:PXD018053
type
dataset
label
GEO PXD018053
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-32935914
type
extraction
used array · 1 item
[0]
source:pmid:32935914
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD018053
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD018053
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:32935914
parent_hash
sha256:e8052348b3b2ac7b2d7e18683629e6fb8a2d7858ca3c4248c6cc2823924635d1
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:PXD018053 licence not read
[1]
asset:data:geo:PXD018053 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 2 items
[0] object · 11 fields
role
data_generation
definition_id
animal_model
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
tissue collected from T1D double transgenic mice were subjected to mass spectrometry-based proteom
[1]
Experimental animal models Twenty transgenic mice were from the ‘Cantacuzino’ National Institute of
[2]
in pancreatic β‐cells. Since the Ins‐HA+/+Tg mice were homozygous and the TCR‐HA± Tg mice were hete
[3]
/+Tg mice were homozygous and the TCR‐HA± Tg mice were heterozygous, the offspring were either Ins–
order_basis
paper_text_order:521
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
mass_spectrometry
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
T1D double transgenic mice were subjected to mass spectrometry-based proteomic analysis, and the results we
[1]
rget in the therapy of diabetic nephropathy. Mass spectrometry data are available via ProteomeXchange with
[2]
cals used for liquid chromatography (LC) and mass spectrometry (MS) experiments were of LC‐MS grade. Trypsi
[3]
4). Preparation of kidney tissue samples for mass spectrometry analysis After solubilization, 50 µg of prot
order_basis
paper_text_order:543
id
assay:2
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32935914", "kind": "science-record", "revision": 6, "content_hash": "sha256:615eba153f01b82de06135934bfbf7f46891fb8e2c9fee2b03039449fbbfae11", "created_at": "2026-11-01T15:41:10Z", "updated_at": "2026-11-01T21:23:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Diabetic nephropathy associates with deregulation of enzymes involved in kidney sulphur metabolism.", "doi": "10.1111/jcmm.15855", "pmid": "32935914", "authors": ["Elena Uyy", "Viorel Iulian Suica", "Raluca Maria Boteanu", "Florentina Safciuc", "Aurel Cerveanu-Hogas", "Luminita Ivan", "Crina Stavaru", "Maya Simionescu", "Felicia Antohe"], "journal": "Journal of cellular and molecular medicine", "year": 2020, "abstract": "Nephropathy is a major chronic complication of diabetes. A crucial role in renal pathophysiology is played by hydrogen sulphide (H2 S) that is produced excessively by the kidney; however, the data regarding H2 S bioavailability are inconsistent. We hypothesize that early type 1 diabetes (T1D) increases H2 S production by a mechanism involving hyperglycaemia-induced alterations in sulphur metabolism. Plasma and kidney tissue collected from T1D double transgenic mice were subjected to mass spectrometry-based proteomic analysis, and the results were validated by immunological and gene expression assays.T1D mice exhibited a high concentration of H2 S in the plasma and kidney tissue and histological, showed signs of subtle kidney fibrosis, characteristic for early renal disease. The shotgun proteomic analyses disclosed that the level of enzymes implicated in sulphate activation modulators, H2 S-oxidation and H2 S-production were significantly affected (ie 6 up-regulated and 4 down-regulated). Gene expression results corroborated well with the proteomic data. Dysregulation of H2 S enzymes underly the changes occurring in H2 S production, which in turn could play a key role in the initiation of renal disease. The new findings lead to a novel target in the therapy of diabetic nephropathy. Mass spectrometry data are available via ProteomeXchange with identifier PXD018053.", "claims": [{"id": "claim-method", "statement": "The results were analysed by Student's unpaired t test using GraphPad Prism 5.0 statistical software (GraphPad Software).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32935914", "locator": "sections[11] \"Statistics\" paragraph 2", "quote": "The results were analysed by Student's unpaired t test using GraphPad Prism 5.0 statistical software (GraphPad Software)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data openly available in a public repository that issues datasets with DOIs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32935914", "locator": "sections[24] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "Data openly available in a public repository that issues datasets with DOIs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32935914"], "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": "complete", "blocked_on": null, "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": ["data:geo:PXD018053"], "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": ["data:geo:PXD018053"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32935914", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/jcmm.15855", "sha256": "sha256:d175ee470cd063cd8d147444ec3340814a22ce57ee736da139d0ff1cdafbb623", "bytes": 43173, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/jcmm.15855", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7579703", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD018053", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD018053", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD018053", "version": null, "note": "Data openly available in a public repository that issues datasets with DOIs.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data openly available in a public repository that issues datasets with DOIs.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Mouse early diabetic nephropathy LC-MS/MS analysis", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32935914:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:686f38007042c821629b0c45b483d1185ffd5e85ab1750c2078cac9bc8b4f3e7", "bytes": 849, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#jcmm15855-tbl-0001", "version": null, "note": "Over‐represented KEGG pathways in diabetic vs non‐diabetic kidney tissue", "structure": {"pmcid": "PMC7579703", "section_index": 15, "section_title": "Modifications of kidney proteome in T1D revealed by global shotgun proteomic analysis", "row_count": 10, "column_count": 3}, "table": {"label": "TABLE 1", "caption": "Over‐represented KEGG pathways in diabetic vs non‐diabetic kidney tissue", "rows": [["No.", "Description", "FDR P‐value"], ["1", "Sulphur metabolism (mmu00920)", "3.46E‐05"], ["2", "Proximal tubule bicarbonate reclamation (mmu04964)", "5.56E‐05"], ["3", "Glycine, serine and threonine metabolism (mmu00260)", "6.40E‐05"], ["4", "Cysteine and methionine metabolism (mmu00270)", "1.08E‐04"], ["5", "Arginine and proline metabolism (mmu00330)", "3.10E‐03"], ["6", "D‐Glutamine and D‐glutamate metabolism (mmu00471)", "3.35E‐03"], ["7", "Seleno‐compound metabolism (mmu00450)", "5.50E‐03"], ["8", "Lysine degradation (mmu00310)", "1.69E‐02"], ["9", "PPAR signalling pathway (mmu03320)", "2.04E‐02"]], "row_count": 10, "column_count": 3, "numeric_cells": 27, "header_rows": 1, "locator": "section[15]/table-wrap[1]#jcmm15855-tbl-0001"}}], "gaps": ["asset:data:geo:PXD018053 not downloaded", "asset:data:geo:PXD018053 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Student's unpaired t test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The results were analysed by Student's unpaired t test using GraphPad Prism 5.0 statistical software (GraphPad Software)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Student's unpaired t test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": "R1", "reachable": true, "accessions": ["PXD018053"], "resolved_accessions": ["PXD018053"], "statements": ["Data openly available in a public repository that issues datasets with DOIs."], "basis": "The paper names PXD018053 in PRIDE and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32935914", "data:geo:PXD018053", "asset:table:pmid:32935914:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD018053"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:29Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 33988, "completion_tokens": 648, "cached_tokens": 792}}, "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:32935914", "type": "paper", "label": "pmid:32935914"}, {"id": "source:pmid:32935914", "type": "manuscript", "label": "PMID 32935914 full text"}, {"id": "data:geo:PXD018053", "type": "dataset", "label": "GEO PXD018053"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32935914", "type": "paper", "label": "pmid:32935914"}, {"id": "source:pmid:32935914", "type": "manuscript", "label": "PMID 32935914 full text"}, {"id": "data:geo:PXD018053", "type": "dataset", "label": "GEO PXD018053"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32935914", "type": "extraction", "used": ["source:pmid:32935914"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD018053", "type": "accession_resolution", "used": ["data:geo:PXD018053"], "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:32935914", "parent_hash": "sha256:e8052348b3b2ac7b2d7e18683629e6fb8a2d7858ca3c4248c6cc2823924635d1", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD018053 licence not read", "asset:data:geo:PXD018053 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tissue collected from T1D double transgenic mice were subjected to mass spectrometry-based proteom", "Experimental animal models Twenty transgenic mice were from the ‘Cantacuzino’ National Institute of", "in pancreatic β‐cells. Since the Ins‐HA+/+Tg mice were homozygous and the TCR‐HA± Tg mice were hete", "/+Tg mice were homozygous and the TCR‐HA± Tg mice were heterozygous, the offspring were either Ins–"], "order_basis": "paper_text_order:521", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["T1D double transgenic mice were subjected to mass spectrometry-based proteomic analysis, and the results we", "rget in the therapy of diabetic nephropathy. Mass spectrometry data are available via ProteomeXchange with", "cals used for liquid chromatography (LC) and mass spectrometry (MS) experiments were of LC‐MS grade. Trypsi", "4). Preparation of kidney tissue samples for mass spectrometry analysis After solubilization, 50 µg of prot"], "order_basis": "paper_text_order:543", "id": "assay:2"}]}