← All .science files
pmid:40005856
Luteolin Alleviates Inflammation Induced by Staphylococcus aureus in Bovine Mammary Epithelial Cells by Attenuating NF-κB and MAPK Activation.
Yingfang Guo · Jinxin Zhang · Ting Yuan · Cheng Yang · Qingqing Zhou · Aftab Shaukat · Ganzhen Deng · Xiaoyan Wang
Veterinary sciences · 2025 doi:10.3390/vetsci12020096
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 8 items
claims array · 2 items
[0] object · 6 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 · 4 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
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 · 4 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 · 4 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 · 0 items
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 · 6 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 4 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40005856", "kind": "science-record", "revision": 4, "content_hash": "sha256:fcb6e10b5704fbebb5dac682407b982d15a288264342b5eb4eeab898fc3181ab", "created_at": "2026-11-01T20:30:14Z", "updated_at": "2026-11-01T22:56:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Luteolin Alleviates Inflammation Induced by Staphylococcus aureus in Bovine Mammary Epithelial Cells by Attenuating NF-κB and MAPK Activation.", "doi": "10.3390/vetsci12020096", "pmid": "40005856", "authors": ["Yingfang Guo", "Jinxin Zhang", "Ting Yuan", "Cheng Yang", "Qingqing Zhou", "Aftab Shaukat", "Ganzhen Deng", "Xiaoyan Wang"], "journal": "Veterinary sciences", "year": 2025, "abstract": "The internalization of S. aureus in bMECs is a major pathogenic mechanism leading to mastitis, causing significant economic losses in the dairy industry. Numerous plants contain Lut, a natural flavonoid with anti-inflammatory and antioxidant properties. However, little is known about Lut's ability to reduce inflammation caused by S. aureus in bMECs. This research aimed to evaluate the mechanism by which Lut reduces S. aureus-induced inflammation in bMECs. Through GO and KEGG enrichment analysis, researchers analyzed the differentially expressed genes in bMECs infected with S. aureus in NCBI GEO (GSE139612) and also analyzed the targets of Lut predicted by various online platforms. These studies identified two overlapping signaling pathways, the NF-κB and the MAPK pathways. We stimulated bMECs with S. aureus for two hours and then added Lut for ten hours, with a total duration of twelve hours. The expression levels of TLR2-MyD88-TRAF6 components, inflammatory cytokines, and protein phosphorylation associated with the MAPK and NF-κB signaling pathways were then assessed. Based on all of the results, Lut inhibited the generation of inflammatory cytokines in bMECs that were induced by S. aureus through the TLR2, NF-κB, and MAPK signaling pathways. This process might account for the anti-inflammatory properties of Lut.", "claims": [{"id": "claim-method", "statement": "After per-forming the normality test, Student’s t-tests or one-way ANOVA were used to analyze group differences.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40005856", "locator": "sections[11] \"2.9. Data Analysis\" paragraph 2", "quote": "After per-forming the normality test, Student’s t-tests or one-way ANOVA were used to analyze group differences."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are contained within the article and Supplementary Materials.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40005856", "locator": "sections[27] \"notes\" paragraph 1", "quote": "Data are contained within the article and Supplementary Materials."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:40005856"], "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:GSE139612"], "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:GSE139612"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40005856", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/vetsci12020096", "sha256": "sha256:6841c773102f4cffccdd4089e3b59289b1d1e95ed1fede568864c1692a6600c9", "bytes": 24216, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/vetsci12020096", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11861667", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE139612", "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=GSE139612", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE139612", "version": null, "note": "Data are contained within the article and Supplementary Materials.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are contained within the article and Supplementary Materials.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4144695", "GSM4144696", "GSM4144697", "GSM4144698"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "11648", "taxon": "Bos taurus", "title": "Transcriptomic Analysis of Inflammatory Responses in Bovine Mammary Epithelial Cells following Stimulation with Escherichia coli and Staphylococcus aureus", "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:GSE139612 not downloaded", "asset:data:geo:GSE139612 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "After per-forming the normality test, Student’s t-tests or one-way ANOVA were used to analyze group differences."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE139612"], "resolved_accessions": ["GSE139612"], "statements": ["Data are contained within the article and Supplementary Materials."], "basis": "The paper names GSE139612 in NCBI GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:40005856", "data:geo:GSE139612"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE139612"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:47:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 7779, "completion_tokens": 948, "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:40005856", "type": "paper", "label": "pmid:40005856"}, {"id": "source:pmid:40005856", "type": "manuscript", "label": "PMID 40005856 full text"}, {"id": "data:geo:GSE139612", "type": "dataset", "label": "GEO GSE139612"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40005856", "type": "paper", "label": "pmid:40005856"}, {"id": "source:pmid:40005856", "type": "manuscript", "label": "PMID 40005856 full text"}, {"id": "data:geo:GSE139612", "type": "dataset", "label": "GEO GSE139612"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40005856", "type": "extraction", "used": ["source:pmid:40005856"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE139612", "type": "accession_resolution", "used": ["data:geo:GSE139612"], "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:40005856", "parent_hash": "sha256:726f5e32e1bef742b3fa71d43a5e37039618b51b91597e4dffd50e34fb2bf484", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE139612 licence not read", "asset:data:geo:GSE139612 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["After per-forming the normality test, Student’s t-tests or one-way ANOVA were used to analyze group differences."], "order_basis": "analysis_only", "id": "assay:1"}]}