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

pmid:28951444

Quantitative Analysis of Proteome Modulations in Alveolar Epithelial Type II Cells in Response to Pulmonary Aspergillus fumigatus Infection.

Pegah Seddigh · Thilo Bracht · Válerie Molinier-Frenkel · Flavia Castellano · Olaf Kniemeyer · Marc Schuster · Juliane Weski · Anja Hasenberg · Andreas Kraus · Gernot Poschet · Thomas Hager · Dirk Theegarten · Christiane A Opitz · Axel A Brakhage · Barbara Sitek · Mike Hasenberg · Matthias Gunzer

Molecular & cellular proteomics : MCP · 2017 doi:10.1074/mcp.RA117.000072

Paper

complete

Experiment

partial

Data

partial

Analysis

complete

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:28951444
kind
science-record
content_hash
sha256:afd986cb9eb49c2b88dfd6fdde6e4cd295dadabc2582933e08235c71e6344db4
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:28Z
updated_at
2026-11-01T21:59:31Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Quantitative Analysis of Proteome Modulations in Alveolar Epithelial Type II Cells in Response to Pulmonary Aspergillus fumigatus Infection.
doi
10.1074/mcp.RA117.000072
pmid
28951444
authors array · 17 items
[0]
Pegah Seddigh
[1]
Thilo Bracht
[2]
Válerie Molinier-Frenkel
[3]
Flavia Castellano
[4]
Olaf Kniemeyer
[5]
Marc Schuster
[6]
Juliane Weski
[7]
Anja Hasenberg
[8]
Andreas Kraus
[9]
Gernot Poschet
[10]
Thomas Hager
[11]
Dirk Theegarten
[12]
Christiane A Opitz
[13]
Axel A Brakhage
[14]
Barbara Sitek
[15]
Mike Hasenberg
[16]
Matthias Gunzer
journal
Molecular & cellular proteomics : MCP
year
2017
abstract
The ubiquitous mold Aspergillus fumigatus threatens immunosuppressed patients as inducer of lethal invasive aspergillosis. A. fumigatus conidia are airborne and reach the alveoli, where they encounter alveolar epithelial cells (AEC). Previous studies reported the importance of the surfactant-producing AEC II during A. fumigatus infection via in vitro experiments using cell lines. We established a negative isolation protocol yielding untouched primary murine AEC II with a purity >90%, allowing ex vivo analyses of the cells, which encountered the mold in vivo By label-free proteome analysis of AEC II isolated from mice 24h after A. fumigatus or mock infection we quantified 2256 proteins and found 154 proteins to be significantly differentially abundant between both groups (ANOVA p value ≤ 0.01, ratio of means ≥1.5 or ≤0.67, quantified with ≥2 peptides). Most of these proteins were higher abundant in the infected condition and reflected a comprehensive activation of AEC II on interaction with A. fumigatus This was especially represented by proteins related to oxidative phosphorylation, hence energy production. However, the most strongly induced protein was the l-amino acid oxidase (LAAO) Interleukin 4 induced 1 (IL4I1) with a 42.9 fold higher abundance (ANOVA p value 2.91-10). IL4I1 has previously been found in B cells, macrophages, dendritic cells and rare neurons. Increased IL4I1 abundance in AEC II was confirmed by qPCR, Western blot and immunohistology. Furthermore, A. fumigatus infected lungs showed high levels of IL4I1 metabolic products. Importantly, higher IL4I1 abundance was also confirmed in lung tissue from human aspergilloma. Because LAAO are key enzymes for bactericidal product generation, AEC II might actively participate in pathogen defense. We provide insights into proteome changes of primary AEC II thereby opening new avenues to analyze the molecular changes of this central lung cell on infectious threats. Data are available via ProteomeXchange with identifier PXD005834.
claims array · 1 item
[0] object · 6 fields
id
claim-target-result
statement
The paper found that IL4I1 was the most strongly induced protein in primary alveolar epithelial type II cells after Aspergillus fumigatus infection, with a 42.9-fold increase; differential protein abundance was assessed by ANOVA, and the proteomics source data are available through ProteomeXchange under identifier PXD005834.
kind
quantitative
target object · 4 fields
value
42.9
unit
fold change
tolerance
null
source
However, the most strongly induced protein was the l-amino acid oxidase (LAAO) Interleukin 4 induced 1 (IL4I1) with a 42.9 fold higher abundance (ANOVA p value 2.91−10).
evidence array · 4 items
[0] object · 3 fields
asset
source:pmid:28951444
locator
sections[0] "Abstract" paragraph 1
quote
Most of these proteins were higher abundant in the infected condition and reflected a comprehensive activation of AEC II on interaction with A. fumigatus.
[1] object · 3 fields
asset
source:pmid:28951444
locator
sections[0] "Abstract" paragraph 1
quote
However, the most strongly induced protein was the l-amino acid oxidase (LAAO) Interleukin 4 induced 1 (IL4I1) with a 42.9 fold higher abundance (ANOVA p value 2.91−10).
[2] object · 3 fields
asset
source:pmid:28951444
locator
sections[0] "Abstract" paragraph 1
quote
By label-free proteome analysis of AEC II isolated from mice 24h after A. fumigatus or mock infection we quantified 2256 proteins and found 154 proteins to be significantly differentially abundant between both groups (ANOVA p value ≤ 0.01, ratio of means ≥1.5 or ≤0.67, quantified with ≥2 peptides).
[3] object · 3 fields
asset
source:pmid:28951444
locator
sections[0] "Abstract" paragraph 1
quote
Data are available via ProteomeXchange with identifier PXD005834.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
The paper found that IL4I1 was the most strongly induced protein in primary alveolar epithelial type II cells after Aspergillus fumigatus infection, with a 42.9-fold increase; differential protein abundance was assessed by ANOVA, and the proteomics source data are available through ProteomeXchange under identifier PXD005834.
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:28951444
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 · 1 field
p_value
ween both groups (ANOVA p value ≤ 0
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:28951444
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1074/mcp.RA117.000072
sha256
sha256:5c651b48597a5c65a842150faff327a042883aab48566210ebbf5120b96440c1
bytes
2034
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1074/mcp.RA117.000072
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
PMC5724180
source
ncbi_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
gaps array · 0 items
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
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 · 1 field
p_value
ween both groups (ANOVA p value ≤ 0
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
0.7
band
medium
quote
ANOVA
targets array · 1 item
[0] object · 8 fields
id
target-published-estimate
claim_id
claim-target-result
operation
bootstrap_mean_difference
unit
fold change
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.
gaps array · 0 items
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 · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
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: anova.
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 · 0 items
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 · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 1 item
[0]
source:pmid:28951444
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
2026-10-31T18:32:32Z
independence
single_reader
evidence_check object · 2 fields
method
null
availability
null
calls
2
usage object · 3 fields
prompt_tokens
1850
completion_tokens
794
cached_tokens
896
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:28951444
type
paper
label
pmid:28951444
[1] object · 3 fields
id
source:pmid:28951444
type
manuscript
label
PMID 28951444 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:28951444
type
paper
label
pmid:28951444
[1] object · 3 fields
id
source:pmid:28951444
type
manuscript
label
PMID 28951444 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-28951444
type
extraction
used array · 1 item
[0]
source:pmid:28951444
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:28951444
parent_hash
sha256:54c3f7573fa16329579c405036ade39c1ec3f94a45c423c62c8f5f08805a0a86
fork_of
null
gaps array · 5 items
[0]
execution.not_run
[1]
review.human_critique
[2]
review.independent_reader
[3]
review.machine_critique
[4]
step:obtain_source_data blocked on data:accession_absent
assays array · 4 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 · 2 items
[0]
solation protocol yielding untouched primary murine AEC II with a purity >90%, allowing ex vivo
[1]
ses of the cells, which encountered the mold in vivo By label-free proteome analysis of AEC II is
order_basis
paper_text_order:551
id
assay:1
[1] object · 11 fields
role
data_generation
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]
d IL4I1 abundance in AEC II was confirmed by qPCR, Western blot and immunohistology. Furthermo
order_basis
paper_text_order:1535
id
assay:2
[2] 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]
1 abundance in AEC II was confirmed by qPCR, Western blot and immunohistology. Furthermore, A. fumigat
order_basis
paper_text_order:1541
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
ANOVA
order_basis
consumes_earlier_output
id
assay:4
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28951444", "kind": "science-record", "revision": 4, "content_hash": "sha256:afd986cb9eb49c2b88dfd6fdde6e4cd295dadabc2582933e08235c71e6344db4", "created_at": "2026-11-01T15:40:28Z", "updated_at": "2026-11-01T21:59:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative Analysis of Proteome Modulations in Alveolar Epithelial Type II Cells in Response to Pulmonary Aspergillus fumigatus Infection.", "doi": "10.1074/mcp.RA117.000072", "pmid": "28951444", "authors": ["Pegah Seddigh", "Thilo Bracht", "Válerie Molinier-Frenkel", "Flavia Castellano", "Olaf Kniemeyer", "Marc Schuster", "Juliane Weski", "Anja Hasenberg", "Andreas Kraus", "Gernot Poschet", "Thomas Hager", "Dirk Theegarten", "Christiane A Opitz", "Axel A Brakhage", "Barbara Sitek", "Mike Hasenberg", "Matthias Gunzer"], "journal": "Molecular & cellular proteomics : MCP", "year": 2017, "abstract": "The ubiquitous mold Aspergillus fumigatus threatens immunosuppressed patients as inducer of lethal invasive aspergillosis. A. fumigatus conidia are airborne and reach the alveoli, where they encounter alveolar epithelial cells (AEC). Previous studies reported the importance of the surfactant-producing AEC II during A. fumigatus infection via in vitro experiments using cell lines. We established a negative isolation protocol yielding untouched primary murine AEC II with a purity >90%, allowing ex vivo analyses of the cells, which encountered the mold in vivo By label-free proteome analysis of AEC II isolated from mice 24h after A. fumigatus or mock infection we quantified 2256 proteins and found 154 proteins to be significantly differentially abundant between both groups (ANOVA p value ≤ 0.01, ratio of means ≥1.5 or ≤0.67, quantified with ≥2 peptides). Most of these proteins were higher abundant in the infected condition and reflected a comprehensive activation of AEC II on interaction with A. fumigatus This was especially represented by proteins related to oxidative phosphorylation, hence energy production. However, the most strongly induced protein was the l-amino acid oxidase (LAAO) Interleukin 4 induced 1 (IL4I1) with a 42.9 fold higher abundance (ANOVA p value 2.91-10). IL4I1 has previously been found in B cells, macrophages, dendritic cells and rare neurons. Increased IL4I1 abundance in AEC II was confirmed by qPCR, Western blot and immunohistology. Furthermore, A. fumigatus infected lungs showed high levels of IL4I1 metabolic products. Importantly, higher IL4I1 abundance was also confirmed in lung tissue from human aspergilloma. Because LAAO are key enzymes for bactericidal product generation, AEC II might actively participate in pathogen defense. We provide insights into proteome changes of primary AEC II thereby opening new avenues to analyze the molecular changes of this central lung cell on infectious threats. Data are available via ProteomeXchange with identifier PXD005834.", "claims": [{"id": "claim-target-result", "statement": "The paper found that IL4I1 was the most strongly induced protein in primary alveolar epithelial type II cells after Aspergillus fumigatus infection, with a 42.9-fold increase; differential protein abundance was assessed by ANOVA, and the proteomics source data are available through ProteomeXchange under identifier PXD005834.", "kind": "quantitative", "target": {"value": 42.9, "unit": "fold change", "tolerance": null, "source": "However, the most strongly induced protein was the l-amino acid oxidase (LAAO) Interleukin 4 induced 1 (IL4I1) with a 42.9 fold higher abundance (ANOVA p value 2.91−10)."}, "evidence": [{"asset": "source:pmid:28951444", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Most of these proteins were higher abundant in the infected condition and reflected a comprehensive activation of AEC II on interaction with A. fumigatus."}, {"asset": "source:pmid:28951444", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "However, the most strongly induced protein was the l-amino acid oxidase (LAAO) Interleukin 4 induced 1 (IL4I1) with a 42.9 fold higher abundance (ANOVA p value 2.91−10)."}, {"asset": "source:pmid:28951444", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "By label-free proteome analysis of AEC II isolated from mice 24h after A. fumigatus or mock infection we quantified 2256 proteins and found 154 proteins to be significantly differentially abundant between both groups (ANOVA p value ≤ 0.01, ratio of means ≥1.5 or ≤0.67, quantified with ≥2 peptides)."}, {"asset": "source:pmid:28951444", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD005834."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper found that IL4I1 was the most strongly induced protein in primary alveolar epithelial type II cells after Aspergillus fumigatus infection, with a 42.9-fold increase; differential protein abundance was assessed by ANOVA, and the proteomics source data are available through ProteomeXchange under identifier PXD005834.", "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:28951444"], "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": {"p_value": "ween both groups (ANOVA p value ≤ 0"}, "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:28951444", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1074/mcp.RA117.000072", "sha256": "sha256:5c651b48597a5c65a842150faff327a042883aab48566210ebbf5120b96440c1", "bytes": 2034, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1074/mcp.RA117.000072", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5724180", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": {"p_value": "ween both groups (ANOVA p value ≤ 0"}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.7, "band": "medium", "quote": "ANOVA"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 42.9, "unit": "fold change", "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."}], "gaps": []}, "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": [], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:28951444"], "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": "2026-10-31T18:32:32Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 2, "usage": {"prompt_tokens": 1850, "completion_tokens": 794, "cached_tokens": 896}}, "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:28951444", "type": "paper", "label": "pmid:28951444"}, {"id": "source:pmid:28951444", "type": "manuscript", "label": "PMID 28951444 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28951444", "type": "paper", "label": "pmid:28951444"}, {"id": "source:pmid:28951444", "type": "manuscript", "label": "PMID 28951444 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28951444", "type": "extraction", "used": ["source:pmid:28951444"], "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:28951444", "parent_hash": "sha256:54c3f7573fa16329579c405036ade39c1ec3f94a45c423c62c8f5f08805a0a86", "fork_of": null, "generation": 3}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": ["solation protocol yielding untouched primary murine AEC II with a purity >90%, allowing ex vivo", "ses of the cells, which encountered the mold in vivo By label-free proteome analysis of AEC II is"], "order_basis": "paper_text_order:551", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["d IL4I1 abundance in AEC II was confirmed by qPCR, Western blot and immunohistology. Furthermo"], "order_basis": "paper_text_order:1535", "id": "assay:2"}, {"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": ["1 abundance in AEC II was confirmed by qPCR, Western blot and immunohistology. Furthermore, A. fumigat"], "order_basis": "paper_text_order:1541", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["ANOVA"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}