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

pmid:35095494

MicroRNA-92a-3p Enhances Cisplatin Resistance by Regulating Krüppel-Like Factor 4-Mediated Cell Apoptosis and Epithelial-to-Mesenchymal Transition in Cervical Cancer.

Jing Yang · Jing Hai · Xuecai Dong · Mengjie Zhang · Shufeng Duan

Frontiers in pharmacology · 2021 doi:10.3389/fphar.2021.783213

Paper

complete

Experiment

partial

Data

partial

Analysis

partial

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:35095494
kind
science-record
content_hash
sha256:f7f3dd1f1397af9d92935e1fc49b2079f98308875b353503915a6e87cd2be64a
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T17:36:49Z
updated_at
2026-11-01T22:48:19Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
MicroRNA-92a-3p Enhances Cisplatin Resistance by Regulating Krüppel-Like Factor 4-Mediated Cell Apoptosis and Epithelial-to-Mesenchymal Transition in Cervical Cancer.
doi
10.3389/fphar.2021.783213
pmid
35095494
authors array · 5 items
[0]
Jing Yang
[1]
Jing Hai
[2]
Xuecai Dong
[3]
Mengjie Zhang
[4]
Shufeng Duan
journal
Frontiers in pharmacology
year
2021
abstract
Recent studies have confirmed the existence and key roles of microRNA (miRNAs) in cancer drug resistance, including cervical cancer (CC). The present study aims to establish a novel role for miR-92a-3p and its associated gene networks in cisplatin (DDP) resistance of CC. First, the disparities in miRNA expression between CC tissues and adjacent normal tissues were screened based on GSE19611 microarray data that retrieved from Gene Expression Omnibus (GEO), and we identified several miRs that were significantly downregulated or upregulated in CC tissues including miR-92a-3p. Moreover, miR-92a-3p was significantly up-regulated in DDP-resistant cells and was the most differently expressed miRNA. Functionally, knockdown of miR-92a-3p increased the sensitivity of DDP-resistant cells to DDP via inhibiting cell proliferation, migration and invasion, and promoting apoptosis. Conversely, overexpression of miR-92a-3p significantly induced DDP resistance in CC parental cells including HeLa and SiHa cells. Moreover, Krüppel-like factor 4 (KLF4) was identified as a direct target of miR-92a-3p, and an obvious inverse correlation was observed between the expression of miR-92a-3p and KLF4 in 40 pairs of cancer tissues. Furthermore, KLF4 knockdown reversed the promoting effect of miR-92a-3p inhibition on DDP sensitivity in DDP-resistant CC cells. Besides, high expression of miR-92a-3p was associated with DDP resistance, as well as a short overall survival in clinic. Taken together, these findings provide important evidence that miR-92a-3p targets KLF4 and is significant in DDP resistance in CC, indicating that miR-92a-3p may be an attractive target to increase DDP sensitivity in clinical CC treatment.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Differentially expressed miRNAs (DE-miRNAs) between CC tissue samples and adjacent normal tissues were screened based on GEO2R (www.ncbi.nlm.nih.gov/geo/geo2r/), an interactive web tool. The criterion for DE-miRNAs has been set as |fold change| > 1.5 and p < 0.01.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:35095494
locator
sections[4] "MicroRNA Expression Profile Data From GEO" paragraph 2
quote
Differentially expressed miRNAs (DE-miRNAs) between CC tissue samples and adjacent normal tissues were screened based on GEO2R (www.ncbi.nlm.nih.gov/geo/geo2r/), an interactive web tool. The criterion for DE-miRNAs has been set as |fold change| > 1.5 and p < 0.01.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:35095494
locator
sections[26] "Data Availability Statement" paragraph 2
quote
The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
miR-92a-3p targets KLF4 and promotes cisplatin resistance in cervical cancer.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:35095494
locator
sections[0] "Abstract" paragraph 1
quote
Taken together, these findings provide important evidence that miR-92a-3p targets KLF4 and is significant in DDP resistance in CC, indicating that miR-92a-3p may be an attractive target to increase DDP sensitivity in clinical CC treatment.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
miR-92a-3p targets KLF4 and promotes cisplatin resistance in cervical cancer.
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:35095494
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:GSE19611
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
blocked
blocked_on
method:student_t
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
ld-change threshold and p-value, followed by unpaired S
inputs array · 1 item
[0]
data:geo:GSE19611
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:run_analysis blocked on method:student_t
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:35095494
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3389/fphar.2021.783213
sha256
sha256:697fd46f71164531e52a56ab8907704adacfba1127d492ada99a553890c13931
bytes
60970
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3389/fphar.2021.783213
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
PMC8795743
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE19611
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=GSE19611
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE19611
version
null
note
The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.
access_statement_kind
data_availability_statement
sample_accessions array · 43 items
[0]
GSM489127
[1]
GSM489128
[2]
GSM489129
[3]
GSM489130
[4]
GSM489131
[5]
GSM489132
[6]
GSM489133
[7]
GSM489134
[8]
GSM489135
[9]
GSM489136
[10]
GSM489137
[11]
GSM489138
[12]
GSM489139
[13]
GSM489140
[14]
GSM489141
[15]
GSM489142
[16]
GSM489143
[17]
GSM489144
[18]
GSM489145
[19]
GSM489146
[20]
GSM489147
[21]
GSM489148
[22]
GSM489149
[23]
GSM489150
[24]
GSM489151
[25]
GSM489152
[26]
GSM489153
[27]
GSM489154
[28]
GSM489155
[29]
GSM489156
[30]
GSM489157
[31]
GSM489158
[32]
GSM489159
[33]
GSM489160
[34]
GSM489161
[35]
GSM489162
[36]
GSM489163
[37]
GSM489164
[38]
GSM489165
[39]
GSM489166
[40]
GSM489167
[41]
GSM489168
[42]
GSM489169
sample_count
43
group_sizes
null
group_sizes_basis
null
platform
7534
taxon
Homo sapiens; Mus musculus; Rattus norvegicus
title
miRNA profiling in cervical carcinomas, low and high-grade intraepithelial cervical lesions and normal cervical tissues
resolution_checked_at
2026-11-01T18:06:43Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE19611 not downloaded
[1]
asset:data:geo:GSE19611 licence not read
analysis object · 4 fields
state
partial
methods array · 2 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
student_t_test
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
student_t
expressible
false
parameters object · 1 field
p_value
ld-change threshold and p-value, followed by unpaired S
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
Differentially expressed miRNAs (DE-miRNAs) between CC tissue samples and adjacent normal tissues were screened based on GEO2R (www.ncbi.nlm.nih.gov/geo/geo2r/), an interactive web tool. The criterion for DE-miRNAs has been set as |fold change| > 1.5 and p < 0.01.
[1] object · 10 fields
id
method-2
family
survival_analysis
specific
kaplan_meier
label
Survival analysis
dsl_operations array · 1 item
[0]
survival_km
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.8
band
high
quote
Kaplan-Meier
targets array · 0 items
gaps array · 2 items
[0]
method.reader_differs_from_extractor
[1]
method.student_t
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
false
required_operations array · 0 items
missing_operations array · 1 item
[0]
student_t
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test.
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]
GSE19611
resolved_accessions array · 1 item
[0]
GSE19611
statements array · 1 item
[0]
The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.
basis
The paper names GSE19611 in Gene Expression Omnibus (GEO) 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:35095494
[1]
data:geo:GSE19611
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
operation
student_t
priority
null
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE19611
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
2026-11-01T17:31:11Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
19296
completion_tokens
1157
cached_tokens
0
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:35095494
type
paper
label
pmid:35095494
[1] object · 3 fields
id
source:pmid:35095494
type
manuscript
label
PMID 35095494 full text
[2] object · 3 fields
id
data:geo:GSE19611
type
dataset
label
GEO GSE19611
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:35095494
type
paper
label
pmid:35095494
[1] object · 3 fields
id
source:pmid:35095494
type
manuscript
label
PMID 35095494 full text
[2] object · 3 fields
id
data:geo:GSE19611
type
dataset
label
GEO GSE19611
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-35095494
type
extraction
used array · 1 item
[0]
source:pmid:35095494
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE19611
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE19611
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:35095494
parent_hash
sha256:62c1d9315f82649d19d3b7fc367580ccc442bd218dcd878733895d11c06e12fd
fork_of
null
gaps array · 9 items
[0]
asset:data:geo:GSE19611 licence not read
[1]
asset:data:geo:GSE19611 not downloaded
[2]
execution.not_run
[3]
method.reader_differs_from_extractor
[4]
method.student_t
[5]
review.human_critique
[6]
review.independent_reader
[7]
review.machine_critique
[8]
step:run_analysis blocked on method:student_t
assays array · 4 items
[0] 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
0.99
evidence array · 3 items
[0]
gulating Krüppel-Like Factor 4-Mediated Cell Apoptosis and Epithelial-to-Mesenchymal Transition in
[1]
ation, migration and invasion, and promoting apoptosis. Conversely, overexpression of miR-92a-3p si
[2]
ls were detected by the Cell Counting Kit-8 (CCK-8) assay (Sigma-Aldrich; Merck KGaA) to determ
order_basis
paper_text_order:51
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
transfection
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]
t differently expressed miRNA. Functionally, knockdown of miR-92a-3p increased the sensitivity of D
[1]
0 pairs of cancer tissues. Furthermore, KLF4 knockdown reversed the promoting effect of miR-92a-3p
[2]
ibitor + DDP (10 μM) + si-KLF4 group. During transfection, the cells (2×105 cells/well) were plated in
[3]
d into 6-well culture plates. The cells were transfected using Lipofectamine™ 2000 (Invitrogen; Therm
order_basis
paper_text_order:838
id
assay:2
[2] 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]
DP resistance in CC parental cells including HeLa and SiHa cells. Moreover, Krüppel-like facto
[1]
from ATCC (Manassas, VA, United States) and cultured in DMEM (Dulbecco’s minimum essential medium) c
[2]
ubator with 5% CO2. HeLa and SiHa cells were cultured in increasing concentrations of DDP (Sigma, St.
[3]
nd Treatment Two cervical cancer cell lines (HeLa and SiHa) were purchased from ATCC (Manassas
order_basis
paper_text_order:1111
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Differentially expressed miRNAs (DE-miRNAs) between CC tissue samples and adjacent normal tissues were screened based on GEO2R (www.ncbi.nlm.nih.gov/geo/geo2r/), an interactive web tool. The criterion for DE-miRNAs has been set as |fold change| > 1.5 and p < 0.01.
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:35095494", "kind": "science-record", "revision": 6, "content_hash": "sha256:f7f3dd1f1397af9d92935e1fc49b2079f98308875b353503915a6e87cd2be64a", "created_at": "2026-11-01T17:36:49Z", "updated_at": "2026-11-01T22:48:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "MicroRNA-92a-3p Enhances Cisplatin Resistance by Regulating Krüppel-Like Factor 4-Mediated Cell Apoptosis and Epithelial-to-Mesenchymal Transition in Cervical Cancer.", "doi": "10.3389/fphar.2021.783213", "pmid": "35095494", "authors": ["Jing Yang", "Jing Hai", "Xuecai Dong", "Mengjie Zhang", "Shufeng Duan"], "journal": "Frontiers in pharmacology", "year": 2021, "abstract": "Recent studies have confirmed the existence and key roles of microRNA (miRNAs) in cancer drug resistance, including cervical cancer (CC). The present study aims to establish a novel role for miR-92a-3p and its associated gene networks in cisplatin (DDP) resistance of CC. First, the disparities in miRNA expression between CC tissues and adjacent normal tissues were screened based on GSE19611 microarray data that retrieved from Gene Expression Omnibus (GEO), and we identified several miRs that were significantly downregulated or upregulated in CC tissues including miR-92a-3p. Moreover, miR-92a-3p was significantly up-regulated in DDP-resistant cells and was the most differently expressed miRNA. Functionally, knockdown of miR-92a-3p increased the sensitivity of DDP-resistant cells to DDP via inhibiting cell proliferation, migration and invasion, and promoting apoptosis. Conversely, overexpression of miR-92a-3p significantly induced DDP resistance in CC parental cells including HeLa and SiHa cells. Moreover, Krüppel-like factor 4 (KLF4) was identified as a direct target of miR-92a-3p, and an obvious inverse correlation was observed between the expression of miR-92a-3p and KLF4 in 40 pairs of cancer tissues. Furthermore, KLF4 knockdown reversed the promoting effect of miR-92a-3p inhibition on DDP sensitivity in DDP-resistant CC cells. Besides, high expression of miR-92a-3p was associated with DDP resistance, as well as a short overall survival in clinic. Taken together, these findings provide important evidence that miR-92a-3p targets KLF4 and is significant in DDP resistance in CC, indicating that miR-92a-3p may be an attractive target to increase DDP sensitivity in clinical CC treatment.", "claims": [{"id": "claim-method", "statement": "Differentially expressed miRNAs (DE-miRNAs) between CC tissue samples and adjacent normal tissues were screened based on GEO2R (www.ncbi.nlm.nih.gov/geo/geo2r/), an interactive web tool. The criterion for DE-miRNAs has been set as |fold change| > 1.5 and p < 0.01.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35095494", "locator": "sections[4] \"MicroRNA Expression Profile Data From GEO\" paragraph 2", "quote": "Differentially expressed miRNAs (DE-miRNAs) between CC tissue samples and adjacent normal tissues were screened based on GEO2R (www.ncbi.nlm.nih.gov/geo/geo2r/), an interactive web tool. The criterion for DE-miRNAs has been set as |fold change| > 1.5 and p < 0.01."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35095494", "locator": "sections[26] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "miR-92a-3p targets KLF4 and promotes cisplatin resistance in cervical cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35095494", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Taken together, these findings provide important evidence that miR-92a-3p targets KLF4 and is significant in DDP resistance in CC, indicating that miR-92a-3p may be an attractive target to increase DDP sensitivity in clinical CC treatment."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "miR-92a-3p targets KLF4 and promotes cisplatin resistance in cervical cancer.", "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:35095494"], "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:GSE19611"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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": "ld-change threshold and p-value, followed by unpaired S"}, "inputs": ["data:geo:GSE19611"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35095494", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fphar.2021.783213", "sha256": "sha256:697fd46f71164531e52a56ab8907704adacfba1127d492ada99a553890c13931", "bytes": 60970, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fphar.2021.783213", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8795743", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19611", "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=GSE19611", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19611", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM489127", "GSM489128", "GSM489129", "GSM489130", "GSM489131", "GSM489132", "GSM489133", "GSM489134", "GSM489135", "GSM489136", "GSM489137", "GSM489138", "GSM489139", "GSM489140", "GSM489141", "GSM489142", "GSM489143", "GSM489144", "GSM489145", "GSM489146", "GSM489147", "GSM489148", "GSM489149", "GSM489150", "GSM489151", "GSM489152", "GSM489153", "GSM489154", "GSM489155", "GSM489156", "GSM489157", "GSM489158", "GSM489159", "GSM489160", "GSM489161", "GSM489162", "GSM489163", "GSM489164", "GSM489165", "GSM489166", "GSM489167", "GSM489168", "GSM489169"], "sample_count": 43, "group_sizes": null, "group_sizes_basis": null, "platform": "7534", "taxon": "Homo sapiens; Mus musculus; Rattus norvegicus", "title": "miRNA profiling in cervical carcinomas, low and high-grade intraepithelial cervical lesions and normal cervical tissues", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE19611 not downloaded", "asset:data:geo:GSE19611 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {"p_value": "ld-change threshold and p-value, followed by unpaired S"}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed miRNAs (DE-miRNAs) between CC tissue samples and adjacent normal tissues were screened based on GEO2R (www.ncbi.nlm.nih.gov/geo/geo2r/), an interactive web tool. The criterion for DE-miRNAs has been set as |fold change| > 1.5 and p < 0.01."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor", "method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE19611"], "resolved_accessions": ["GSE19611"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE19611 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:35095494", "data:geo:GSE19611"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19611"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:31:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 19296, "completion_tokens": 1157, "cached_tokens": 0}}, "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:35095494", "type": "paper", "label": "pmid:35095494"}, {"id": "source:pmid:35095494", "type": "manuscript", "label": "PMID 35095494 full text"}, {"id": "data:geo:GSE19611", "type": "dataset", "label": "GEO GSE19611"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35095494", "type": "paper", "label": "pmid:35095494"}, {"id": "source:pmid:35095494", "type": "manuscript", "label": "PMID 35095494 full text"}, {"id": "data:geo:GSE19611", "type": "dataset", "label": "GEO GSE19611"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35095494", "type": "extraction", "used": ["source:pmid:35095494"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19611", "type": "accession_resolution", "used": ["data:geo:GSE19611"], "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:35095494", "parent_hash": "sha256:62c1d9315f82649d19d3b7fc367580ccc442bd218dcd878733895d11c06e12fd", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE19611 licence not read", "asset:data:geo:GSE19611 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["gulating Krüppel-Like Factor 4-Mediated Cell Apoptosis and Epithelial-to-Mesenchymal Transition in", "ation, migration and invasion, and promoting apoptosis. Conversely, overexpression of miR-92a-3p si", "ls were detected by the Cell Counting Kit-8 (CCK-8) assay (Sigma-Aldrich; Merck KGaA) to determ"], "order_basis": "paper_text_order:51", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["t differently expressed miRNA. Functionally, knockdown of miR-92a-3p increased the sensitivity of D", "0 pairs of cancer tissues. Furthermore, KLF4 knockdown reversed the promoting effect of miR-92a-3p", "ibitor + DDP (10 μM) + si-KLF4 group. During transfection, the cells (2×105 cells/well) were plated in", "d into 6-well culture plates. The cells were transfected using Lipofectamine™ 2000 (Invitrogen; Therm"], "order_basis": "paper_text_order:838", "id": "assay:2"}, {"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": ["DP resistance in CC parental cells including HeLa and SiHa cells. Moreover, Krüppel-like facto", "from ATCC (Manassas, VA, United States) and cultured in DMEM (Dulbecco’s minimum essential medium) c", "ubator with 5% CO2. HeLa and SiHa cells were cultured in increasing concentrations of DDP (Sigma, St.", "nd Treatment Two cervical cancer cell lines (HeLa and SiHa) were purchased from ATCC (Manassas"], "order_basis": "paper_text_order:1111", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed miRNAs (DE-miRNAs) between CC tissue samples and adjacent normal tissues were screened based on GEO2R (www.ncbi.nlm.nih.gov/geo/geo2r/), an interactive web tool. The criterion for DE-miRNAs has been set as |fold change| > 1.5 and p < 0.01."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}