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

pmid:30462321

ZEB2, a master regulator of the epithelial-mesenchymal transition, mediates trophoblast differentiation.

Sonia C DaSilva-Arnold · Che-Ying Kuo · Viralkumar Davra · Yvonne Remache · Peter C W Kim · John P Fisher · Stacy Zamudio · Abdulla Al-Khan · Raymond B Birge · Nicholas P Illsley

Molecular human reproduction · 2019 doi:10.1093/molehr/gay053

Paper

complete

Experiment

complete

Data

partial

Analysis

absent

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:30462321
kind
science-record
content_hash
sha256:05630d046cfa74995fb1f625537d89db7822107dd695db12f2bc95a30033c78c
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T17:32:28Z
updated_at
2026-11-01T18:50:04Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
ZEB2, a master regulator of the epithelial-mesenchymal transition, mediates trophoblast differentiation.
doi
10.1093/molehr/gay053
pmid
30462321
authors array · 10 items
[0]
Sonia C DaSilva-Arnold
[1]
Che-Ying Kuo
[2]
Viralkumar Davra
[3]
Yvonne Remache
[4]
Peter C W Kim
[5]
John P Fisher
[6]
Stacy Zamudio
[7]
Abdulla Al-Khan
[8]
Raymond B Birge
[9]
Nicholas P Illsley
journal
Molecular human reproduction
year
2019
abstract
STUDY QUESTION: Does the upregulation of the zinc finger E-box binding homeobox 2 (ZEB2) transcription factor in human trophoblast cells lead to alterations in gene expression consistent with an epithelial-mesenchymal transition (EMT) and a consequent increase in invasiveness? SUMMARY ANSWER: Overexpression of ZEB2 results in an epithelial-mesenchymal shift in gene expression accompanied by a substantial increase in the invasive capacity of human trophoblast cells. WHAT IS KNOWN ALREADY: In-vivo results have shown that cytotrophoblast differentiation into extravillous trophoblast involves an epithelial-mesenchymal transition. The only EMT master regulatory factor which shows changes consistent with extravillous trophoblast EMT status and invasive capacity is the ZEB2 transcription factor. STUDY DESIGN, SIZE, DURATION: This study is a mechanistic investigation of the role of ZEB2 in trophoblast differentiation. We generated stable ZEB2 overexpression clones using the epithelial BeWo and JEG3 choriocarcinoma lines. Using these clones, we investigated the effects of ZEB2 overexpression on the expression of EMT-associated genes and proteins, cell morphology and invasive capability. PARTICIPANTS/MATERIALS, SETTING, METHODS: We used lentiviral transduction to overexpress ZEB2 in BeWo and JEG3 cells. Stable clones were selected based on ZEB2 expression and morphology. A PCR array of EMT-associated genes was used to probe gene expression. Protein measurements were performed by western blotting. Gain-of-function was assessed by quantitatively measuring cell invasion rates using a Transwell assay, a 3D bioprinted placenta model and the xCelligenceTM platform. MAIN RESULTS AND THE ROLE OF CHANCE: The four selected clones (2 × BeWo, 2 × JEG3, based on ZEB2 expression and morphology) all showed gene expression changes indicative of an EMT. The two clones (1 × BeWo, 1 × JEG3) showing >40-fold increase in ZEB2 expression also displayed increased ZEB2 protein; the others, with increases in ZEB2 expression <14-fold did not. The two high ZEB2-expressing clones demonstrated robust increases in invasive capacity, as assessed by three types of invasion assay. These data identify ZEB2-mediated transcription as a key mechanism transforming the epithelial-like trophoblast into cells with a mesenchymal, invasive phenotype. LARGE SCALE DATA: PCR array data have been deposited in the GEO database under accession number GSE116532. LIMITATIONS, REASONS FOR CAUTION: These are in-vitro studies using choriocarcinoma cells and so the results should be interpreted in view of these limitations. Nevertheless, the data are consistent with in-vivo findings and are replicated in two different cell lines. WIDER IMPLICATIONS OF THE FINDINGS: The combination of these data with the in-vivo findings clearly identify ZEB2-mediated EMT as the mechanism for cytotrophoblast differentiation into extravillous trophoblast. Having characterized these cellular mechanisms, it will now be possible to identify the intracellular and extracellular regulatory components which control ZEB2 and trophoblast differentiation. It will also be possible to identify the aberrant factors which alter differentiation in invasive pathologies such as preeclampsia and abnormally invasive placenta (AKA accreta, increta, percreta). STUDY FUNDING AND COMPETING INTEREST(s): Funding was provided by the Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine and Surgery at Hackensack Meridian Health, Hackensack, NJ. The 3D bioprinted placental model work done in Drs Kim and Fisher's labs was supported by the Children's National Medical Center. The xCELLigence work done in Dr Birge's lab was supported by NIH CA165077. The authors declare no competing interests.
claims array · 2 items
[0] object · 6 fields
id
claim-data-access
statement
PCR array data have been deposited in the GEO database under accession number GSE116532.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:30462321
locator
sections[0] "Abstract" paragraph 7
quote
PCR array data have been deposited in the GEO database under accession number GSE116532.
state
complete
[1] object · 6 fields
id
claim-target-result
statement
Overexpression of ZEB2 results in an epithelial–mesenchymal shift in gene expression accompanied by a substantial increase in the invasive capacity of human trophoblast cells.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:30462321
locator
sections[0] "Abstract" paragraph 2
quote
Overexpression of ZEB2 results in an epithelial–mesenchymal shift in gene expression accompanied by a substantial increase in the invasive capacity of human trophoblast cells.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
Overexpression of ZEB2 results in an epithelial–mesenchymal shift in gene expression accompanied by a substantial increase in the invasive capacity of human trophoblast cells.
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:30462321
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:GSE116532
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:GSE116532
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 · 2 items
[0] object · 15 fields
id
source:pmid:30462321
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1093/molehr/gay053
sha256
sha256:e036f21ce45a10a39a427c4b0550608b15d29a65d8fb4e013760a13cd75ee20a
bytes
3491
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1093/molehr/gay053
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
PMC6497037
source
ncbi_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE116532
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=GSE116532
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE116532
version
null
note
PCR array data have been deposited in the GEO database under accession number GSE116532.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
PCR array data have been deposited in the GEO database under accession number GSE116532.
access_statement_kind
data_availability_statement
sample_accessions array · 18 items
[0]
GSM3242404
[1]
GSM3242405
[2]
GSM3242406
[3]
GSM3242407
[4]
GSM3242408
[5]
GSM3242409
[6]
GSM3242410
[7]
GSM3242411
[8]
GSM3242412
[9]
GSM3242413
[10]
GSM3242414
[11]
GSM3242415
[12]
GSM3242416
[13]
GSM3242417
[14]
GSM3242418
[15]
GSM3242419
[16]
GSM3242420
[17]
GSM3242421
sample_count
18
group_sizes
null
group_sizes_basis
null
platform
20702
taxon
Homo sapiens
title
ZEB2, a master regulator of the epithelial-mesenchymal transition, mediates trophoblast differentiation
resolution_checked_at
2026-11-01T17:30:42Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE116532 not downloaded
[1]
asset:data:geo:GSE116532 licence not read
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
operations
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 (not named), 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]
GSE116532
resolved_accessions array · 1 item
[0]
GSE116532
statements array · 1 item
[0]
PCR array data have been deposited in the GEO database under accession number GSE116532.
basis
The paper names GSE116532 in GEO database 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 · 2 items
[0]
source:pmid:30462321
[1]
data:geo:GSE116532
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:GSE116532
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
2026-11-01T16:58:02Z
independence
single_reader
evidence_check object · 2 fields
method
null
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
2325
completion_tokens
524
cached_tokens
128
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:30462321
type
paper
label
pmid:30462321
[1] object · 3 fields
id
source:pmid:30462321
type
manuscript
label
PMID 30462321 full text
[2] object · 3 fields
id
data:geo:GSE116532
type
dataset
label
GEO GSE116532
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:30462321
type
paper
label
pmid:30462321
[1] object · 3 fields
id
source:pmid:30462321
type
manuscript
label
PMID 30462321 full text
[2] object · 3 fields
id
data:geo:GSE116532
type
dataset
label
GEO GSE116532
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-30462321
type
extraction
used array · 1 item
[0]
source:pmid:30462321
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE116532
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE116532
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:30462321
parent_hash
sha256:18719f9600cb0ba2221ab2ea511b3a983851aa388bb8ee3bf39c147291ca9163
fork_of
null
gaps array · 8 items
[0]
asset:data:geo:GSE116532 licence not read
[1]
asset:data:geo:GSE116532 not downloaded
[2]
execution.not_run
[3]
method
[4]
operations
[5]
review.human_critique
[6]
review.independent_reader
[7]
review.machine_critique
assays array · 1 item
[0] object · 11 fields
role
data_generation
definition_id
western_blot
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
sion. Protein measurements were performed by western blotting. Gain-of-function was assessed by quantitati
order_basis
paper_text_order:1554
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30462321", "kind": "science-record", "revision": 2, "content_hash": "sha256:05630d046cfa74995fb1f625537d89db7822107dd695db12f2bc95a30033c78c", "created_at": "2026-11-01T17:32:28Z", "updated_at": "2026-11-01T18:50:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "ZEB2, a master regulator of the epithelial-mesenchymal transition, mediates trophoblast differentiation.", "doi": "10.1093/molehr/gay053", "pmid": "30462321", "authors": ["Sonia C DaSilva-Arnold", "Che-Ying Kuo", "Viralkumar Davra", "Yvonne Remache", "Peter C W Kim", "John P Fisher", "Stacy Zamudio", "Abdulla Al-Khan", "Raymond B Birge", "Nicholas P Illsley"], "journal": "Molecular human reproduction", "year": 2019, "abstract": "STUDY QUESTION: Does the upregulation of the zinc finger E-box binding homeobox 2 (ZEB2) transcription factor in human trophoblast cells lead to alterations in gene expression consistent with an epithelial-mesenchymal transition (EMT) and a consequent increase in invasiveness?\nSUMMARY ANSWER: Overexpression of ZEB2 results in an epithelial-mesenchymal shift in gene expression accompanied by a substantial increase in the invasive capacity of human trophoblast cells.\nWHAT IS KNOWN ALREADY: In-vivo results have shown that cytotrophoblast differentiation into extravillous trophoblast involves an epithelial-mesenchymal transition. The only EMT master regulatory factor which shows changes consistent with extravillous trophoblast EMT status and invasive capacity is the ZEB2 transcription factor.\nSTUDY DESIGN, SIZE, DURATION: This study is a mechanistic investigation of the role of ZEB2 in trophoblast differentiation. We generated stable ZEB2 overexpression clones using the epithelial BeWo and JEG3 choriocarcinoma lines. Using these clones, we investigated the effects of ZEB2 overexpression on the expression of EMT-associated genes and proteins, cell morphology and invasive capability.\nPARTICIPANTS/MATERIALS, SETTING, METHODS: We used lentiviral transduction to overexpress ZEB2 in BeWo and JEG3 cells. Stable clones were selected based on ZEB2 expression and morphology. A PCR array of EMT-associated genes was used to probe gene expression. Protein measurements were performed by western blotting. Gain-of-function was assessed by quantitatively measuring cell invasion rates using a Transwell assay, a 3D bioprinted placenta model and the xCelligenceTM platform.\nMAIN RESULTS AND THE ROLE OF CHANCE: The four selected clones (2 × BeWo, 2 × JEG3, based on ZEB2 expression and morphology) all showed gene expression changes indicative of an EMT. The two clones (1 × BeWo, 1 × JEG3) showing >40-fold increase in ZEB2 expression also displayed increased ZEB2 protein; the others, with increases in ZEB2 expression <14-fold did not. The two high ZEB2-expressing clones demonstrated robust increases in invasive capacity, as assessed by three types of invasion assay. These data identify ZEB2-mediated transcription as a key mechanism transforming the epithelial-like trophoblast into cells with a mesenchymal, invasive phenotype.\nLARGE SCALE DATA: PCR array data have been deposited in the GEO database under accession number GSE116532.\nLIMITATIONS, REASONS FOR CAUTION: These are in-vitro studies using choriocarcinoma cells and so the results should be interpreted in view of these limitations. Nevertheless, the data are consistent with in-vivo findings and are replicated in two different cell lines.\nWIDER IMPLICATIONS OF THE FINDINGS: The combination of these data with the in-vivo findings clearly identify ZEB2-mediated EMT as the mechanism for cytotrophoblast differentiation into extravillous trophoblast. Having characterized these cellular mechanisms, it will now be possible to identify the intracellular and extracellular regulatory components which control ZEB2 and trophoblast differentiation. It will also be possible to identify the aberrant factors which alter differentiation in invasive pathologies such as preeclampsia and abnormally invasive placenta (AKA accreta, increta, percreta).\nSTUDY FUNDING AND COMPETING INTEREST(s): Funding was provided by the Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine and Surgery at Hackensack Meridian Health, Hackensack, NJ. The 3D bioprinted placental model work done in Drs Kim and Fisher's labs was supported by the Children's National Medical Center. The xCELLigence work done in Dr Birge's lab was supported by NIH CA165077. The authors declare no competing interests.", "claims": [{"id": "claim-data-access", "statement": "PCR array data have been deposited in the GEO database under accession number GSE116532.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30462321", "locator": "sections[0] \"Abstract\" paragraph 7", "quote": "PCR array data have been deposited in the GEO database under accession number GSE116532."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Overexpression of ZEB2 results in an epithelial–mesenchymal shift in gene expression accompanied by a substantial increase in the invasive capacity of human trophoblast cells.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:30462321", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Overexpression of ZEB2 results in an epithelial–mesenchymal shift in gene expression accompanied by a substantial increase in the invasive capacity of human trophoblast cells."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Overexpression of ZEB2 results in an epithelial–mesenchymal shift in gene expression accompanied by a substantial increase in the invasive capacity of human trophoblast cells.", "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:30462321"], "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:GSE116532"], "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:GSE116532"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30462321", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1093/molehr/gay053", "sha256": "sha256:e036f21ce45a10a39a427c4b0550608b15d29a65d8fb4e013760a13cd75ee20a", "bytes": 3491, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1093/molehr/gay053", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6497037", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE116532", "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=GSE116532", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116532", "version": null, "note": "PCR array data have been deposited in the GEO database under accession number GSE116532.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "PCR array data have been deposited in the GEO database under accession number GSE116532.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3242404", "GSM3242405", "GSM3242406", "GSM3242407", "GSM3242408", "GSM3242409", "GSM3242410", "GSM3242411", "GSM3242412", "GSM3242413", "GSM3242414", "GSM3242415", "GSM3242416", "GSM3242417", "GSM3242418", "GSM3242419", "GSM3242420", "GSM3242421"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "20702", "taxon": "Homo sapiens", "title": "ZEB2, a master regulator of the epithelial-mesenchymal transition, mediates trophoblast differentiation", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE116532 not downloaded", "asset:data:geo:GSE116532 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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 (not named), 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": ["GSE116532"], "resolved_accessions": ["GSE116532"], "statements": ["PCR array data have been deposited in the GEO database under accession number GSE116532."], "basis": "The paper names GSE116532 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:30462321", "data:geo:GSE116532"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE116532"]}, "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": "2026-11-01T16:58:02Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 2325, "completion_tokens": 524, "cached_tokens": 128}}, "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:30462321", "type": "paper", "label": "pmid:30462321"}, {"id": "source:pmid:30462321", "type": "manuscript", "label": "PMID 30462321 full text"}, {"id": "data:geo:GSE116532", "type": "dataset", "label": "GEO GSE116532"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30462321", "type": "paper", "label": "pmid:30462321"}, {"id": "source:pmid:30462321", "type": "manuscript", "label": "PMID 30462321 full text"}, {"id": "data:geo:GSE116532", "type": "dataset", "label": "GEO GSE116532"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30462321", "type": "extraction", "used": ["source:pmid:30462321"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE116532", "type": "accession_resolution", "used": ["data:geo:GSE116532"], "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:30462321", "parent_hash": "sha256:18719f9600cb0ba2221ab2ea511b3a983851aa388bb8ee3bf39c147291ca9163", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE116532 licence not read", "asset:data:geo:GSE116532 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["sion. Protein measurements were performed by western blotting. Gain-of-function was assessed by quantitati"], "order_basis": "paper_text_order:1554", "id": "assay:1"}]}