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

pmid:41023503

Hypoxia-drives reversible cell cycle arrest in lung cancer cells via modulation of cellular redox and gene expression.

Dharmendra Kumar Maurya · Varshita Mehta · Babita Singh

Medical oncology (Northwood, London, England) · 2025 doi:10.1007/s12032-025-03058-9

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:41023503
kind
science-record
content_hash
sha256:80c5b6d7766e62f5ff31faa173f1abcab190d758aeccfe0220bf5b394a8461d8
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:31:05Z
updated_at
2026-11-01T21:35:49Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Hypoxia-drives reversible cell cycle arrest in lung cancer cells via modulation of cellular redox and gene expression.
doi
10.1007/s12032-025-03058-9
pmid
41023503
authors array · 3 items
[0]
Dharmendra Kumar Maurya
[1]
Varshita Mehta
[2]
Babita Singh
journal
Medical oncology (Northwood, London, England)
year
2025
abstract
Hypoxia is a well-recognized clinical feature of solid tumors, including lung cancer, and is associated with poor prognosis due to its role in promoting resistance to chemotherapy and radiotherapy. To investigate the cellular consequences of hypoxia, we cultured A549 lung adenocarcinoma cells under 1% O2 and examined their growth, cell cycle distribution, and redox status. Hypoxia significantly reduces cell proliferation and induced G1 phase cell cycle arrest, suggesting a cytostatic effect. Biochemical analysis showed a 2.64- and 2.04-fold increase in total and mitochondrial reactive oxygen species (ROS) levels, respectively, along with an elevated total thiol levels under hypoxic conditions compared to normoxia. To assess the reversibility of the hypoxic response, we performed a reciprocal oxygen exposure experiment where cells initially grown under hypoxia were re-exposed to normoxia, and vice versa. To explore the underlying molecular mechanism, we analyzed transcriptomic datasets (GEO accession: GSE48134 and GSE42416) which revealed that hypoxia downregulated key genes involved in energy metabolism (e.g., PDK4, G6PD), cell cycle progression (e.g., CCND1, CDK2), and redox regulation (e.g., GCLM, TXNRD1, NQO1, GCLC). Further, few of redox-related genes were validated by RT-PCR in A549 cells cultured under hypoxia and normoxia for 24 h. Importantly, cyclic hypoxia (intermittent hypoxia-reoxygenation) conditions showed partial restoration of some of these transcripts, supporting the transient nature of hypoxic stress, consistent with our in vitro observations. Furthermore, transcriptome profiles from adenocarcinoma patients (GEO accession: GSE30979) also match our cell line observations. Thus, our results clearly show that hypoxia causes a temporary cell cycle arrest in lung cancer cells, which is reversible when oxygen is restored.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
The data obtained from the cell viability and cell proliferation assays, the cell cycle, redox status apoptosis assay, and the cell proliferation assay were analyzed using multiple comparison analysis followed by Tukey’s post-hoc test.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41023503
locator
sections[11] "Statistical analysis" paragraph 2
quote
The data obtained from the cell viability and cell proliferation assays, the cell cycle, redox status apoptosis assay, and the cell proliferation assay were analyzed using multiple comparison analysis followed by Tukey’s post-hoc test.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
No datasets were generated or analysed during the current study.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41023503
locator
sections[25] "Data availability" paragraph 2
quote
No datasets were generated or analysed during the current study.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
Thus, our results clearly show that hypoxia causes a temporary cell cycle arrest in lung cancer cells, which is reversible when oxygen is restored.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41023503
locator
sections[0] "Abstract" paragraph 1
quote
Thus, our results clearly show that hypoxia causes a temporary cell cycle arrest in lung cancer cells, which is reversible when oxygen is restored.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
Thus, our results clearly show that hypoxia causes a temporary cell cycle arrest in lung cancer cells, which is reversible when oxygen is restored.
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:41023503
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:GSE30979
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:GSE30979
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 · 4 items
[0] object · 15 fields
id
source:pmid:41023503
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1007/s12032-025-03058-9
sha256
sha256:8ad2524466089c09306a086bb0011036252ebc049380ee0c0f531fa86ac6982a
bytes
43996
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1007/s12032-025-03058-9
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
PMC12479581
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE30979
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=GSE30979
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE30979
version
null
note
No datasets were generated or analysed during the current study.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
No datasets were generated or analysed during the current study.
access_statement_kind
data_availability_statement
sample_accessions array · 20 items
[0]
GSM767776
[1]
GSM767777
[2]
GSM767778
[3]
GSM767779
[4]
GSM767780
[5]
GSM767781
[6]
GSM767782
[7]
GSM767783
[8]
GSM767784
[9]
GSM767785
[10]
GSM767786
[11]
GSM767787
[12]
GSM767788
[13]
GSM767789
[14]
GSM767790
[15]
GSM767791
[16]
GSM767792
[17]
GSM767793
[18]
GSM767794
[19]
GSM767795
sample_count
20
group_sizes
null
group_sizes_basis
null
platform
6244
taxon
Homo sapiens
title
Gene expression in hypoxic non-small cell lung cancer
resolution_checked_at
2026-11-01T20:16:08Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 15 fields
id
data:geo:GSE42416
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=GSE42416
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE42416
version
null
note
No datasets were generated or analysed during the current study.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
No datasets were generated or analysed during the current study.
access_statement_kind
data_availability_statement
sample_accessions array · 60 items
[0]
GSM1039631
[1]
GSM1039632
[2]
GSM1039633
[3]
GSM1039634
[4]
GSM1039635
[5]
GSM1039636
[6]
GSM1039637
[7]
GSM1039638
[8]
GSM1039639
[9]
GSM1039640
[10]
GSM1039641
[11]
GSM1039642
[12]
GSM1039643
[13]
GSM1039644
[14]
GSM1039645
[15]
GSM1039646
[16]
GSM1039647
[17]
GSM1039648
[18]
GSM1039649
[19]
GSM1039650
[20]
GSM1039651
[21]
GSM1039652
[22]
GSM1039653
[23]
GSM1039654
[24]
GSM1039655
[25]
GSM1039656
[26]
GSM1039657
[27]
GSM1039658
[28]
GSM1039659
[29]
GSM1039660
[30]
GSM1039661
[31]
GSM1039662
[32]
GSM1039663
[33]
GSM1039664
[34]
GSM1039665
[35]
GSM1039666
[36]
GSM1039667
[37]
GSM1039668
[38]
GSM1039669
[39]
GSM1039670
[40]
GSM1039671
[41]
GSM1039672
[42]
GSM1039673
[43]
GSM1039674
[44]
GSM1039675
[45]
GSM1039676
[46]
GSM1039677
[47]
GSM1039678
[48]
GSM1039679
[49]
GSM1039680
[50]
GSM1039681
[51]
GSM1039682
[52]
GSM1039683
[53]
GSM1039684
[54]
GSM1039685
[55]
GSM1039686
[56]
GSM1039687
[57]
GSM1039688
[58]
GSM1039689
[59]
GSM1039690
sample_count
60
group_sizes
null
group_sizes_basis
null
platform
6244
taxon
Homo sapiens
title
High prognostic potential of a transcriptomic signature related to cycling hypoxia: direct application to breast cancer profiling
resolution_checked_at
2026-11-01T20:16:08Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[3] object · 15 fields
id
data:geo:GSE48134
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=GSE48134
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE48134
version
null
note
No datasets were generated or analysed during the current study.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
No datasets were generated or analysed during the current study.
access_statement_kind
data_availability_statement
sample_accessions array · 15 items
[0]
GSM1169207
[1]
GSM1169208
[2]
GSM1169209
[3]
GSM1169210
[4]
GSM1169211
[5]
GSM1169212
[6]
GSM1169213
[7]
GSM1169214
[8]
GSM1169215
[9]
GSM1169216
[10]
GSM1169217
[11]
GSM1169218
[12]
GSM1169219
[13]
GSM1169220
[14]
GSM1169221
sample_count
15
group_sizes
null
group_sizes_basis
null
platform
6244
taxon
Homo sapiens
title
Designed Oligooxopiperazines as Modulators of Hypoxia-Inducible Factor Signaling
resolution_checked_at
2026-11-01T20:16:08Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 6 items
[0]
asset:data:geo:GSE30979 not downloaded
[1]
asset:data:geo:GSE30979 licence not read
[2]
asset:data:geo:GSE42416 not downloaded
[3]
asset:data:geo:GSE42416 licence not read
[4]
asset:data:geo:GSE48134 not downloaded
[5]
asset:data:geo:GSE48134 licence not read
analysis object · 4 fields
state
partial
methods array · 2 items
[0] object · 10 fields
id
method-1
family
clustering
specific
hierarchical
label
Clustering
dsl_operations array · 1 item
[0]
hierarchical_cluster
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
feature_matrix
evidence object · 3 fields
score
0.8
band
high
quote
hierarchical clustering
[1] object · 10 fields
id
method-2
family
null
specific
null
label
multiple comparison analysis followed by Tukey’s post-hoc 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 data obtained from the cell viability and cell proliferation assays, the cell cycle, redox status apoptosis assay, and the cell proliferation assay were analyzed using multiple comparison analysis followed by Tukey’s post-hoc test.
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
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 1 item
[0]
hierarchical_cluster
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: hierarchical.
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 · 3 items
[0]
GSE48134
[1]
GSE42416
[2]
GSE30979
resolved_accessions array · 3 items
[0]
GSE48134
[1]
GSE42416
[2]
GSE30979
statements array · 1 item
[0]
No datasets were generated or analysed during the current study.
basis
The paper names GSE48134, GSE42416, GSE30979 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 · 1 item
[0]
hierarchical_cluster
assets array · 2 items
[0]
source:pmid:41023503
[1]
data:geo:GSE30979
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:GSE30979
gaps array · 0 items
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
2026-11-01T20:02:18Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
11795
completion_tokens
1599
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:41023503
type
paper
label
pmid:41023503
[1] object · 3 fields
id
source:pmid:41023503
type
manuscript
label
PMID 41023503 full text
[2] object · 3 fields
id
data:geo:GSE30979
type
dataset
label
GEO GSE30979
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:41023503
type
paper
label
pmid:41023503
[1] object · 3 fields
id
source:pmid:41023503
type
manuscript
label
PMID 41023503 full text
[2] object · 3 fields
id
data:geo:GSE30979
type
dataset
label
GEO GSE30979
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-41023503
type
extraction
used array · 1 item
[0]
source:pmid:41023503
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE30979
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE30979
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:41023503
parent_hash
sha256:64b9512c5199bc231ef160172b20260f7f7c7913b79cbf1a0b71bc77a5511471
fork_of
null
gaps array · 11 items
[0]
asset:data:geo:GSE30979 licence not read
[1]
asset:data:geo:GSE30979 not downloaded
[2]
asset:data:geo:GSE42416 licence not read
[3]
asset:data:geo:GSE42416 not downloaded
[4]
asset:data:geo:GSE48134 licence not read
[5]
asset:data:geo:GSE48134 not downloaded
[6]
execution.not_run
[7]
method.reader_named_unmapped
[8]
review.human_critique
[9]
review.independent_reader
[10]
review.machine_critique
assays array · 4 items
[0] object · 11 fields
role
data_generation
definition_id
cell_culture
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]
ate the cellular consequences of hypoxia, we cultured A549 lung adenocarcinoma cells under 1% O2 a
[1]
ellular consequences of hypoxia, we cultured A549 lung adenocarcinoma cells under 1% O2 and ex
[2]
ox-related genes were validated by RT-PCR in A549 cells cultured under hypoxia and normoxia fo
[3]
treatment with hypoxia The A549 lung cancer cell line was maintained in DMEM supplemented with 10% FBS and 1% pen
order_basis
paper_text_order:328
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
rna_seq
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]
underlying molecular mechanism, we analyzed transcriptomic datasets (GEO accession: GSE48134 and GSE424
[1]
Array in.CEL format) and was analyzed using Transcriptome Analysis Console (TAC, AppliedBiosystems), w
[2]
with our in vitro observations. Furthermore, transcriptome profiles from adenocarcinoma patients (GEO a
[3]
the data from the GEO datasets, GSE48134 for transcriptome analysis of normoxia and hypoxia cultured A5
order_basis
paper_text_order:1051
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
apoptosis_assay
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.69
evidence array · 1 item
[0]
eration assays, the cell cycle, redox status apoptosis assay, and the cell proliferation assay were
order_basis
paper_text_order:4082
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
clustering
definition_version
f2132e96ae6c7a4e
required_operations array · 1 item
[0]
hierarchical_cluster
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
hierarchical clustering
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:41023503", "kind": "science-record", "revision": 2, "content_hash": "sha256:80c5b6d7766e62f5ff31faa173f1abcab190d758aeccfe0220bf5b394a8461d8", "created_at": "2026-11-01T20:31:05Z", "updated_at": "2026-11-01T21:35:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Hypoxia-drives reversible cell cycle arrest in lung cancer cells via modulation of cellular redox and gene expression.", "doi": "10.1007/s12032-025-03058-9", "pmid": "41023503", "authors": ["Dharmendra Kumar Maurya", "Varshita Mehta", "Babita Singh"], "journal": "Medical oncology (Northwood, London, England)", "year": 2025, "abstract": "Hypoxia is a well-recognized clinical feature of solid tumors, including lung cancer, and is associated with poor prognosis due to its role in promoting resistance to chemotherapy and radiotherapy. To investigate the cellular consequences of hypoxia, we cultured A549 lung adenocarcinoma cells under 1% O2 and examined their growth, cell cycle distribution, and redox status. Hypoxia significantly reduces cell proliferation and induced G1 phase cell cycle arrest, suggesting a cytostatic effect. Biochemical analysis showed a 2.64- and 2.04-fold increase in total and mitochondrial reactive oxygen species (ROS) levels, respectively, along with an elevated total thiol levels under hypoxic conditions compared to normoxia. To assess the reversibility of the hypoxic response, we performed a reciprocal oxygen exposure experiment where cells initially grown under hypoxia were re-exposed to normoxia, and vice versa. To explore the underlying molecular mechanism, we analyzed transcriptomic datasets (GEO accession: GSE48134 and GSE42416) which revealed that hypoxia downregulated key genes involved in energy metabolism (e.g., PDK4, G6PD), cell cycle progression (e.g., CCND1, CDK2), and redox regulation (e.g., GCLM, TXNRD1, NQO1, GCLC). Further, few of redox-related genes were validated by RT-PCR in A549 cells cultured under hypoxia and normoxia for 24 h. Importantly, cyclic hypoxia (intermittent hypoxia-reoxygenation) conditions showed partial restoration of some of these transcripts, supporting the transient nature of hypoxic stress, consistent with our in vitro observations. Furthermore, transcriptome profiles from adenocarcinoma patients (GEO accession: GSE30979) also match our cell line observations. Thus, our results clearly show that hypoxia causes a temporary cell cycle arrest in lung cancer cells, which is reversible when oxygen is restored.", "claims": [{"id": "claim-method", "statement": "The data obtained from the cell viability and cell proliferation assays, the cell cycle, redox status apoptosis assay, and the cell proliferation assay were analyzed using multiple comparison analysis followed by Tukey’s post-hoc test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41023503", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "The data obtained from the cell viability and cell proliferation assays, the cell cycle, redox status apoptosis assay, and the cell proliferation assay were analyzed using multiple comparison analysis followed by Tukey’s post-hoc test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "No datasets were generated or analysed during the current study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41023503", "locator": "sections[25] \"Data availability\" paragraph 2", "quote": "No datasets were generated or analysed during the current study."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Thus, our results clearly show that hypoxia causes a temporary cell cycle arrest in lung cancer cells, which is reversible when oxygen is restored.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41023503", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Thus, our results clearly show that hypoxia causes a temporary cell cycle arrest in lung cancer cells, which is reversible when oxygen is restored."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Thus, our results clearly show that hypoxia causes a temporary cell cycle arrest in lung cancer cells, which is reversible when oxygen is restored.", "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:41023503"], "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:GSE30979"], "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:GSE30979"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41023503", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12032-025-03058-9", "sha256": "sha256:8ad2524466089c09306a086bb0011036252ebc049380ee0c0f531fa86ac6982a", "bytes": 43996, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12032-025-03058-9", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12479581", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE30979", "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=GSE30979", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30979", "version": null, "note": "No datasets were generated or analysed during the current study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "No datasets were generated or analysed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM767776", "GSM767777", "GSM767778", "GSM767779", "GSM767780", "GSM767781", "GSM767782", "GSM767783", "GSM767784", "GSM767785", "GSM767786", "GSM767787", "GSM767788", "GSM767789", "GSM767790", "GSM767791", "GSM767792", "GSM767793", "GSM767794", "GSM767795"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression in hypoxic non-small cell lung cancer", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE42416", "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=GSE42416", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE42416", "version": null, "note": "No datasets were generated or analysed during the current study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "No datasets were generated or analysed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1039631", "GSM1039632", "GSM1039633", "GSM1039634", "GSM1039635", "GSM1039636", "GSM1039637", "GSM1039638", "GSM1039639", "GSM1039640", "GSM1039641", "GSM1039642", "GSM1039643", "GSM1039644", "GSM1039645", "GSM1039646", "GSM1039647", "GSM1039648", "GSM1039649", "GSM1039650", "GSM1039651", "GSM1039652", "GSM1039653", "GSM1039654", "GSM1039655", "GSM1039656", "GSM1039657", "GSM1039658", "GSM1039659", "GSM1039660", "GSM1039661", "GSM1039662", "GSM1039663", "GSM1039664", "GSM1039665", "GSM1039666", "GSM1039667", "GSM1039668", "GSM1039669", "GSM1039670", "GSM1039671", "GSM1039672", "GSM1039673", "GSM1039674", "GSM1039675", "GSM1039676", "GSM1039677", "GSM1039678", "GSM1039679", "GSM1039680", "GSM1039681", "GSM1039682", "GSM1039683", "GSM1039684", "GSM1039685", "GSM1039686", "GSM1039687", "GSM1039688", "GSM1039689", "GSM1039690"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "High prognostic potential of a transcriptomic signature related to cycling hypoxia: direct application to breast cancer profiling", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE48134", "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=GSE48134", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48134", "version": null, "note": "No datasets were generated or analysed during the current study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "No datasets were generated or analysed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1169207", "GSM1169208", "GSM1169209", "GSM1169210", "GSM1169211", "GSM1169212", "GSM1169213", "GSM1169214", "GSM1169215", "GSM1169216", "GSM1169217", "GSM1169218", "GSM1169219", "GSM1169220", "GSM1169221"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Designed Oligooxopiperazines as Modulators of Hypoxia-Inducible Factor Signaling", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE30979 not downloaded", "asset:data:geo:GSE30979 licence not read", "asset:data:geo:GSE42416 not downloaded", "asset:data:geo:GSE42416 licence not read", "asset:data:geo:GSE48134 not downloaded", "asset:data:geo:GSE48134 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-2", "family": null, "specific": null, "label": "multiple comparison analysis followed by Tukey’s post-hoc test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The data obtained from the cell viability and cell proliferation assays, the cell cycle, redox status apoptosis assay, and the cell proliferation assay were analyzed using multiple comparison analysis followed by Tukey’s post-hoc test."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["hierarchical_cluster"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: hierarchical."}, "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": ["GSE48134", "GSE42416", "GSE30979"], "resolved_accessions": ["GSE48134", "GSE42416", "GSE30979"], "statements": ["No datasets were generated or analysed during the current study."], "basis": "The paper names GSE48134, GSE42416, GSE30979 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["hierarchical_cluster"], "assets": ["source:pmid:41023503", "data:geo:GSE30979"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE30979"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:02:18Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11795, "completion_tokens": 1599, "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:41023503", "type": "paper", "label": "pmid:41023503"}, {"id": "source:pmid:41023503", "type": "manuscript", "label": "PMID 41023503 full text"}, {"id": "data:geo:GSE30979", "type": "dataset", "label": "GEO GSE30979"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41023503", "type": "paper", "label": "pmid:41023503"}, {"id": "source:pmid:41023503", "type": "manuscript", "label": "PMID 41023503 full text"}, {"id": "data:geo:GSE30979", "type": "dataset", "label": "GEO GSE30979"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41023503", "type": "extraction", "used": ["source:pmid:41023503"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE30979", "type": "accession_resolution", "used": ["data:geo:GSE30979"], "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:41023503", "parent_hash": "sha256:64b9512c5199bc231ef160172b20260f7f7c7913b79cbf1a0b71bc77a5511471", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE30979 licence not read", "asset:data:geo:GSE30979 not downloaded", "asset:data:geo:GSE42416 licence not read", "asset:data:geo:GSE42416 not downloaded", "asset:data:geo:GSE48134 licence not read", "asset:data:geo:GSE48134 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ate the cellular consequences of hypoxia, we cultured A549 lung adenocarcinoma cells under 1% O2 a", "ellular consequences of hypoxia, we cultured A549 lung adenocarcinoma cells under 1% O2 and ex", "ox-related genes were validated by RT-PCR in A549 cells cultured under hypoxia and normoxia fo", "treatment with hypoxia The A549 lung cancer cell line was maintained in DMEM supplemented with 10% FBS and 1% pen"], "order_basis": "paper_text_order:328", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["underlying molecular mechanism, we analyzed transcriptomic datasets (GEO accession: GSE48134 and GSE424", "Array in.CEL format) and was analyzed using Transcriptome Analysis Console (TAC, AppliedBiosystems), w", "with our in vitro observations. Furthermore, transcriptome profiles from adenocarcinoma patients (GEO a", "the data from the GEO datasets, GSE48134 for transcriptome analysis of normoxia and hypoxia cultured A5"], "order_basis": "paper_text_order:1051", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["eration assays, the cell cycle, redox status apoptosis assay, and the cell proliferation assay were"], "order_basis": "paper_text_order:4082", "id": "assay:3"}, {"role": "analysis", "definition_id": "clustering", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["hierarchical_cluster"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["hierarchical clustering"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}