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

pmid:39124625

Identification of Catecholamine and Drug Target α2A-Adrenoceptor in Human Testis and Human Testicular Peritubular Cells.

Welter Harald · Kreitmair Nicole · Schneider Michaela · Herrmann Carola · Schmid Nina · Stepanov Youli · Fröhlich Thomas · Köhn Frank-Michael · Pickl Ulrich · Trottmann Matthias · Mayerhofer Artur

Journal of clinical medicine · 2024 doi:10.3390/jcm13154357

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:39124625
kind
science-record
content_hash
sha256:3677a19b4e4ffb47256d1894aaeeae896245c990163678921f2d8fb1e532dddd
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:29:13Z
updated_at
2026-11-01T21:33:39Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Identification of Catecholamine and Drug Target α2A-Adrenoceptor in Human Testis and Human Testicular Peritubular Cells.
doi
10.3390/jcm13154357
pmid
39124625
authors array · 11 items
[0]
Welter Harald
[1]
Kreitmair Nicole
[2]
Schneider Michaela
[3]
Herrmann Carola
[4]
Schmid Nina
[5]
Stepanov Youli
[6]
Fröhlich Thomas
[7]
Köhn Frank-Michael
[8]
Pickl Ulrich
[9]
Trottmann Matthias
[10]
Mayerhofer Artur
journal
Journal of clinical medicine
year
2024
abstract
Background: Clonidine has been used in clinical medicine, e.g., to treat high blood pressure and other conditions. Animal studies have linked its use to impairments of male reproductive functions, and although only a few reports exist for the human species, such actions may exist in man as well. The underlying reasons and, specifically, possible actions of clonidine at the level of the testis are not known. Introduction: Clonidine is an agonist at the α2A-adrenoceptor (ADRA2A), which, as data bank mining indicated, is expressed by several cells of the human testis. The human testis and most of its cells are, however, not readily accessible to experimental testing. Cells from the peritubular wall compartment (human testicular peritubular cells; HTPCs) are the exception. Methods and Results: As shown by immunohistochemical/immunocytochemical and PCR techniques these cells express ADRA2A and retain expression upon isolation and culture. When tested over a concentration range (1-1000 µM) and 24 h, clonidine did not visibly affect HTPC morphology but significantly stimulated IL6 mRNA levels in a concentration-dependent manner. ELISA measurements of cell culture supernatants confirmed a stimulatory action of clonidine (10 µM) on secreted IL6. When examined in collagen gel contraction assays of HTPCs, clonidine (10 µM) exerted a slight relaxing action, while a proteomic study revealed that clonidine (10 µM) did not significantly change cellular protein abundance of HTPCs after 24 h (data available via ProteomeXchange with identifier PXD052220). Conclusion: Thus, ADRA2A-bearing cells in the human testis are targets for catecholamines and drugs such as clonidine. The results of this HTPCs-focused study only show the tip of the iceberg. It is likely that catecholamines/catecholaminergic drugs have the potential to interfere with human testicular functions.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Statistical analyses of qPCR and ELISA data were performed using GraphPad Prism 6.0 Software (GraphPad Software Inc., San Diego, CA, USA). qPCR data were analyzed via t-test of 2−ΔΔCq values, as were IL6 levels in the supernatant via one-sample t-tests of non-normalized values. Paired t-test was used to compare two groups.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:39124625
locator
sections[9] "2.7. Statistical Analysis" paragraph 2
quote
Statistical analyses of qPCR and ELISA data were performed using GraphPad Prism 6.0 Software (GraphPad Software Inc., San Diego, CA, USA). qPCR data were analyzed via t-test of 2−ΔΔCq values, as were IL6 levels in the supernatant via one-sample t-tests of non-normalized values. Paired t-test was used to compare two groups.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD052220.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:39124625
locator
sections[25] "notes" paragraph 1
quote
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD052220.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
Results revealed that only IL6 levels were significantly and more than twofold increased, while all others were unaffected by the 10 µM clonidine treatment for 24 h.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:39124625
locator
sections[14] "3.4. Effect of 10 µM Clonidine on Typical HTPCs Transcripts and IL6 Secretion" paragraph 2
quote
Results revealed that only IL6 levels were significantly and more than twofold increased, while all others were unaffected by the 10 µM clonidine treatment for 24 h (Figure 4).
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
Results revealed that only IL6 levels were significantly and more than twofold increased, while all others were unaffected by the 10 µM clonidine treatment for 24 h.
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:39124625
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:PXD052220
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:PXD052220
outputs array · 1 item
[0]
the replicated result and its comparison
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:39124625
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3390/jcm13154357
sha256
sha256:30228cd5d0d9c5a2e86b93134db27f46011525e67a80fc095386d9e7ba376791
bytes
32020
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3390/jcm13154357
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
PMC11313226
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD052220
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=PXD052220
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD052220
version
null
note
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD052220.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD052220.
access_statement_kind
data_availability_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
Identification of a catecholamine- and drug-target, the α2A-adrenoceptor, in human testis and human testicular perit-ubular cells
resolution_checked_at
2026-11-01T20:16:17Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:PXD052220 not downloaded
[1]
asset:data:geo:PXD052220 licence not read
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
null
specific
null
label
t-test of 2−ΔΔCq values; one-sample t-tests of non-normalized IL6 supernatant values; and paired t-test
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
Statistical analyses of qPCR and ELISA data were performed using GraphPad Prism 6.0 Software (GraphPad Software Inc., San Diego, CA, USA). qPCR data were analyzed via t-test of 2−ΔΔCq values, as were IL6 levels in the supernatant via one-sample t-tests of non-normalized values. Paired t-test was used to compare two groups.
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
blocked
tier
R4
blocking_axis
method
blocked_on
method:not_determinable
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (t-test of 2−ΔΔCq values; one-sample t-tests of non-normalized IL6 supernatant values; and paired t-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
PXD052220
resolved_accessions array · 1 item
[0]
PXD052220
statements array · 1 item
[0]
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD052220.
basis
The paper names PXD052220 in ProteomeXchange Consortium via the PRIDE partner repository 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:39124625
[1]
data:geo:PXD052220
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:PXD052220
gaps array · 1 item
[0]
method:not_determinable
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-11-01T19:27:13Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
10163
completion_tokens
1366
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:39124625
type
paper
label
pmid:39124625
[1] object · 3 fields
id
source:pmid:39124625
type
manuscript
label
PMID 39124625 full text
[2] object · 3 fields
id
data:geo:PXD052220
type
dataset
label
GEO PXD052220
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:39124625
type
paper
label
pmid:39124625
[1] object · 3 fields
id
source:pmid:39124625
type
manuscript
label
PMID 39124625 full text
[2] object · 3 fields
id
data:geo:PXD052220
type
dataset
label
GEO PXD052220
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-39124625
type
extraction
used array · 1 item
[0]
source:pmid:39124625
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD052220
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD052220
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:39124625
parent_hash
sha256:9e67e87b2fd2678cc072490a4b14981541bd0f78f567463d9320486e4031e7b5
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:PXD052220 licence not read
[1]
asset:data:geo:PXD052220 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 6 items
[0] 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
0.99
evidence array · 2 items
[0]
exception. Methods and Results: As shown by immunohistochemical/immunocytochemical and PCR techniques these
[1]
was used for the isolation of HTPCs and for immunohistochemical experiments as described earlier [22]. The s
order_basis
paper_text_order:890
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
0.99
evidence array · 2 items
[0]
levels in a concentration-dependent manner. ELISA measurements of cell culture supernatants co
[1]
al Analysis Statistical analyses of qPCR and ELISA data were performed using GraphPad Prism 6.0
order_basis
paper_text_order:1217
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
clinical_cohort
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]
d (n = 3/experiment), whereas two additional patients were included for qPCR and proteomic analyses (n
[1]
ity assays were conducted with three further patient-derived cells not used in the aforementioned experim
order_basis
paper_text_order:2728
id
assay:3
[3] 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
0.99
evidence array · 4 items
[0]
as two additional patients were included for qPCR and proteomic analyses (n = 5/experiment). I
[1]
our donors (three of which were also used in qPCR studies), while cell contractility assays we
[2]
Statistical Analysis Statistical analyses of qPCR and ELISA data were performed using GraphPad
[3]
GraphPad Software Inc., San Diego, CA, USA). qPCR data were analyzed via t-test of 2−ΔΔCq valu
order_basis
paper_text_order:2755
id
assay:4
[4] 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
0.77
evidence array · 1 item
[0]
ensity of 2.5 × 105 cells per 60 mm dish—and cultured in Dulbecco’s Modified Eagle Medium high glucos
order_basis
paper_text_order:3223
id
assay:5
[5] 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
0.642
evidence array · 1 item
[0]
actility of the epididymis or capsule of the rat testis as well [13,24]. 2.7. Statistical Ana
order_basis
paper_text_order:4155
id
assay:6
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39124625", "kind": "science-record", "revision": 2, "content_hash": "sha256:3677a19b4e4ffb47256d1894aaeeae896245c990163678921f2d8fb1e532dddd", "created_at": "2026-11-01T20:29:13Z", "updated_at": "2026-11-01T21:33:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Catecholamine and Drug Target α2A-Adrenoceptor in Human Testis and Human Testicular Peritubular Cells.", "doi": "10.3390/jcm13154357", "pmid": "39124625", "authors": ["Welter Harald", "Kreitmair Nicole", "Schneider Michaela", "Herrmann Carola", "Schmid Nina", "Stepanov Youli", "Fröhlich Thomas", "Köhn Frank-Michael", "Pickl Ulrich", "Trottmann Matthias", "Mayerhofer Artur"], "journal": "Journal of clinical medicine", "year": 2024, "abstract": "Background: Clonidine has been used in clinical medicine, e.g., to treat high blood pressure and other conditions. Animal studies have linked its use to impairments of male reproductive functions, and although only a few reports exist for the human species, such actions may exist in man as well. The underlying reasons and, specifically, possible actions of clonidine at the level of the testis are not known. Introduction: Clonidine is an agonist at the α2A-adrenoceptor (ADRA2A), which, as data bank mining indicated, is expressed by several cells of the human testis. The human testis and most of its cells are, however, not readily accessible to experimental testing. Cells from the peritubular wall compartment (human testicular peritubular cells; HTPCs) are the exception. Methods and Results: As shown by immunohistochemical/immunocytochemical and PCR techniques these cells express ADRA2A and retain expression upon isolation and culture. When tested over a concentration range (1-1000 µM) and 24 h, clonidine did not visibly affect HTPC morphology but significantly stimulated IL6 mRNA levels in a concentration-dependent manner. ELISA measurements of cell culture supernatants confirmed a stimulatory action of clonidine (10 µM) on secreted IL6. When examined in collagen gel contraction assays of HTPCs, clonidine (10 µM) exerted a slight relaxing action, while a proteomic study revealed that clonidine (10 µM) did not significantly change cellular protein abundance of HTPCs after 24 h (data available via ProteomeXchange with identifier PXD052220). Conclusion: Thus, ADRA2A-bearing cells in the human testis are targets for catecholamines and drugs such as clonidine. The results of this HTPCs-focused study only show the tip of the iceberg. It is likely that catecholamines/catecholaminergic drugs have the potential to interfere with human testicular functions.", "claims": [{"id": "claim-method", "statement": "Statistical analyses of qPCR and ELISA data were performed using GraphPad Prism 6.0 Software (GraphPad Software Inc., San Diego, CA, USA). qPCR data were analyzed via t-test of 2−ΔΔCq values, as were IL6 levels in the supernatant via one-sample t-tests of non-normalized values. Paired t-test was used to compare two groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39124625", "locator": "sections[9] \"2.7. Statistical Analysis\" paragraph 2", "quote": "Statistical analyses of qPCR and ELISA data were performed using GraphPad Prism 6.0 Software (GraphPad Software Inc., San Diego, CA, USA). qPCR data were analyzed via t-test of 2−ΔΔCq values, as were IL6 levels in the supernatant via one-sample t-tests of non-normalized values. Paired t-test was used to compare two groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD052220.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39124625", "locator": "sections[25] \"notes\" paragraph 1", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD052220."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Results revealed that only IL6 levels were significantly and more than twofold increased, while all others were unaffected by the 10 µM clonidine treatment for 24 h.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39124625", "locator": "sections[14] \"3.4. Effect of 10 µM Clonidine on Typical HTPCs Transcripts and IL6 Secretion\" paragraph 2", "quote": "Results revealed that only IL6 levels were significantly and more than twofold increased, while all others were unaffected by the 10 µM clonidine treatment for 24 h (Figure 4)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Results revealed that only IL6 levels were significantly and more than twofold increased, while all others were unaffected by the 10 µM clonidine treatment for 24 h.", "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:39124625"], "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:PXD052220"], "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:PXD052220"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39124625", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/jcm13154357", "sha256": "sha256:30228cd5d0d9c5a2e86b93134db27f46011525e67a80fc095386d9e7ba376791", "bytes": 32020, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/jcm13154357", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11313226", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD052220", "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=PXD052220", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD052220", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD052220.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD052220.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Identification of a catecholamine- and drug-target, the α2A-adrenoceptor, in human testis and human testicular perit-ubular cells", "resolution_checked_at": "2026-11-01T20:16:17Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD052220 not downloaded", "asset:data:geo:PXD052220 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "t-test of 2−ΔΔCq values; one-sample t-tests of non-normalized IL6 supernatant values; and paired t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Statistical analyses of qPCR and ELISA data were performed using GraphPad Prism 6.0 Software (GraphPad Software Inc., San Diego, CA, USA). qPCR data were analyzed via t-test of 2−ΔΔCq values, as were IL6 levels in the supernatant via one-sample t-tests of non-normalized values. Paired t-test was used to compare two groups."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (t-test of 2−ΔΔCq values; one-sample t-tests of non-normalized IL6 supernatant values; and paired t-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD052220"], "resolved_accessions": ["PXD052220"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD052220."], "basis": "The paper names PXD052220 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:39124625", "data:geo:PXD052220"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD052220"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:27:13Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10163, "completion_tokens": 1366, "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:39124625", "type": "paper", "label": "pmid:39124625"}, {"id": "source:pmid:39124625", "type": "manuscript", "label": "PMID 39124625 full text"}, {"id": "data:geo:PXD052220", "type": "dataset", "label": "GEO PXD052220"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39124625", "type": "paper", "label": "pmid:39124625"}, {"id": "source:pmid:39124625", "type": "manuscript", "label": "PMID 39124625 full text"}, {"id": "data:geo:PXD052220", "type": "dataset", "label": "GEO PXD052220"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39124625", "type": "extraction", "used": ["source:pmid:39124625"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD052220", "type": "accession_resolution", "used": ["data:geo:PXD052220"], "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:39124625", "parent_hash": "sha256:9e67e87b2fd2678cc072490a4b14981541bd0f78f567463d9320486e4031e7b5", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:PXD052220 licence not read", "asset:data:geo:PXD052220 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["exception. Methods and Results: As shown by immunohistochemical/immunocytochemical and PCR techniques these", "was used for the isolation of HTPCs and for immunohistochemical experiments as described earlier [22]. The s"], "order_basis": "paper_text_order:890", "id": "assay:1"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["levels in a concentration-dependent manner. ELISA measurements of cell culture supernatants co", "al Analysis Statistical analyses of qPCR and ELISA data were performed using GraphPad Prism 6.0"], "order_basis": "paper_text_order:1217", "id": "assay:2"}, {"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d (n = 3/experiment), whereas two additional patients were included for qPCR and proteomic analyses (n", "ity assays were conducted with three further patient-derived cells not used in the aforementioned experim"], "order_basis": "paper_text_order:2728", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["as two additional patients were included for qPCR and proteomic analyses (n = 5/experiment). I", "our donors (three of which were also used in qPCR studies), while cell contractility assays we", "Statistical Analysis Statistical analyses of qPCR and ELISA data were performed using GraphPad", "GraphPad Software Inc., San Diego, CA, USA). qPCR data were analyzed via t-test of 2−ΔΔCq valu"], "order_basis": "paper_text_order:2755", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ensity of 2.5 × 105 cells per 60 mm dish—and cultured in Dulbecco’s Modified Eagle Medium high glucos"], "order_basis": "paper_text_order:3223", "id": "assay:5"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.642, "evidence": ["actility of the epididymis or capsule of the rat testis as well [13,24]. 2.7. Statistical Ana"], "order_basis": "paper_text_order:4155", "id": "assay:6"}]}