← All .science files
pmid:40551681
Neuroprotective Proteins in Hypoxia-stressed Astrocyte-Derived Extracellular Vesicles.
Berenice N Bernal-Vicente · Isaac Ponce · Manuel Santos-Gutierrez · Emmanuel Ríos-Castro · Luis B Tovar-Y-Romo
Current neuropharmacology · 2025 doi:10.2174/011570159X359837250611052037
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
paper object · 10 fields
authors array · 5 items
claims array · 3 items
[0] object · 6 fields
evidence array · 2 items
[0] object · 3 fields
[1] object · 6 fields
[2] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
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
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 0 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
steps array · 1 item
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
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 7 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40551681", "kind": "science-record", "revision": 2, "content_hash": "sha256:38c232a5910bc7e69809cbab7dc00d069066bd9daadd709fe1077ce1c7986072", "created_at": "2026-11-01T20:30:38Z", "updated_at": "2026-11-01T21:35:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Neuroprotective Proteins in Hypoxia-stressed Astrocyte-Derived Extracellular Vesicles.", "doi": "10.2174/011570159X359837250611052037", "pmid": "40551681", "authors": ["Berenice N Bernal-Vicente", "Isaac Ponce", "Manuel Santos-Gutierrez", "Emmanuel Ríos-Castro", "Luis B Tovar-Y-Romo"], "journal": "Current neuropharmacology", "year": 2025, "abstract": "BACKGROUND: Advances in mass spectrometry-based proteomic analysis have generated extensive protein data from cells involved in neurodegenerative diseases. The field of neuroproteomics is expanding to include the study of extracellular vesicles (EVs) to identify potential biomarkers for disease prevention and endogenous factors involved in neuroprotection.\nMETHODS: In this study, rat cortical astrocytes in normoxia were cultured under normoxic conditions and subsequently exposed to hypoxia. Astrocyte-derived EVs released into the supernatant were collected separately from both conditions. Label-free mass spectrometry-based proteomics was then performed to assess the effects of hypoxia on the EV protein cargo. A meta-analysis comparing the results with previously published EV proteomic datasets was also conducted.\nRESULTS: This study revealed a differential expression of 83 upregulated proteins under hypoxic conditions and 61 downregulated proteins under normoxic conditions, highlighting the protective protein signatures elicited by astrocytes. The dataset has been deposited in the ProteomeXchange Consortium with the identified PXD050160.\nCONCLUSION: The present study makes a novel contribution by employing proteomic techniques to characterize the protein cargo of EVs isolated from primary rat astrocytes. This approach enables a more refined analysis of astrocyte-specific intercellular signaling under hypoxic conditions and provides valuable insights into the roles of astrocytes in maintaining brain homeostasis and contributing to pathological processes.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was performed using a two-sample t-test, and p-value correction (FDR) was applied using the Benjamini-Hochberg procedure. The Simpson index was used for meta-analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40551681", "locator": "sections[9] \"MS-Data Analysis\" paragraph 3", "quote": "Differential expression analysis was performed using a two-sample t-test, and p-value correction (FDR) was applied using the Benjamini-Hochberg procedure."}, {"asset": "source:pmid:40551681", "locator": "sections[10] \"Data Mapping\" paragraph 2", "quote": "The Simpson index was used for meta-analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data and supportive information are available within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40551681", "locator": "sections[26] \"AVAILABILITY OF DATA AND MATERIALS\" paragraph 2", "quote": "The data and supportive information are available within the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This study revealed a differential expression of 83 upregulated proteins under hypoxic conditions and 61 downregulated proteins under normoxic conditions, highlighting the protective protein signatures elicited by astrocytes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40551681", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "This study revealed a differential expression of 83 upregulated proteins under hypoxic conditions and 61 downregulated proteins under normoxic conditions, highlighting the protective protein signatures elicited by astrocytes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This study revealed a differential expression of 83 upregulated proteins under hypoxic conditions and 61 downregulated proteins under normoxic conditions, highlighting the protective protein signatures elicited by astrocytes.", "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:40551681"], "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:PXD050160"], "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:PXD050160"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40551681", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2174/011570159X359837250611052037", "sha256": "sha256:8384e475030323a2631dc330c42ab053c02a43d42f37555554fff600884755ec", "bytes": 66339, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2174/011570159X359837250611052037", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12676041", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD050160", "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=PXD050160", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD050160", "version": null, "note": "The data and supportive information are available within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data and supportive information are available within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic characterization of astrocyte-derived extracellular vesicles under hypoxia", "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:PXD050160 not downloaded", "asset:data:geo:PXD050160 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Two-sample t-test with Benjamini-Hochberg false discovery rate correction; Simpson diversity index for meta-analyses", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "Differential expression analysis was performed using a two-sample t-test, and p-value correction (FDR) was applied using the Benjamini-Hochberg procedure. The Simpson index was used for meta-analyses."}}], "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 (Two-sample t-test with Benjamini-Hochberg false discovery rate correction; Simpson diversity index for meta-analyses), 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": ["PXD050160"], "resolved_accessions": ["PXD050160"], "statements": ["The data and supportive information are available within the article."], "basis": "The paper names PXD050160 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:40551681", "data:geo:PXD050160"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD050160"]}, "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": "2026-11-01T19:54:36Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 18327, "completion_tokens": 1228, "cached_tokens": 256}}, "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:40551681", "type": "paper", "label": "pmid:40551681"}, {"id": "source:pmid:40551681", "type": "manuscript", "label": "PMID 40551681 full text"}, {"id": "data:geo:PXD050160", "type": "dataset", "label": "GEO PXD050160"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40551681", "type": "paper", "label": "pmid:40551681"}, {"id": "source:pmid:40551681", "type": "manuscript", "label": "PMID 40551681 full text"}, {"id": "data:geo:PXD050160", "type": "dataset", "label": "GEO PXD050160"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40551681", "type": "extraction", "used": ["source:pmid:40551681"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD050160", "type": "accession_resolution", "used": ["data:geo:PXD050160"], "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:40551681", "parent_hash": "sha256:30fa03e2a09e946f4946ea9b690f88ffa8cc7bc473b783e2387331384ad2c979", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:PXD050160 licence not read", "asset:data:geo:PXD050160 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["BACKGROUND: Advances in mass spectrometry-based proteomic analysis have generated exte", "separately from both conditions. Label-free mass spectrometry-based proteomics was then performed to asses", "ibed previously [11]. Sample Preparation for Mass Spectrometry EVs suspensions were processed with a protea", "KGROUND: Advances in mass spectrometry-based proteomic analysis have generated extensive protein da"], "order_basis": "paper_text_order:87", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["in neuroprotection. METHODS: In this study, rat cortical astrocytes in normoxia were culture", "e protein cargo of EVs isolated from primary rat astrocytes. This approach enables a more ref", "r the management of biological waste. Wistar rats were used as experimental models for this study.", "r the management of biological waste. Wistar rats were used as experimental models for this st"], "order_basis": "paper_text_order:426", "id": "assay:2"}]}