← All .science files
pmid:34580604
PP2 Ameliorates Renal Fibrosis by Regulating the NF-κB/COX-2 and PPARγ/UCP2 Pathway in Diabetic Mice.
Jinying Wei · Xinna Deng · Yang Li · Runmei Li · Zhaohua Yang · Xiuyuan Li · Shan Song · Yonghong Shi · Huijun Duan · Haijiang Wu
Oxidative medicine and cellular longevity · 2021 doi:10.1155/2021/7394344
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 · 10 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 · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 39 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 10 items
gaps array · 4 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 · 2 items
resolved_accessions array · 2 items
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 · 8 items
assays array · 4 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 · 3 items
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[3] 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:34580604", "kind": "science-record", "revision": 8, "content_hash": "sha256:a5e66e06fa8c9e307015d2c6506f272169b00ad954a213e4dbb2fc43ba839192", "created_at": "2026-11-01T15:41:54Z", "updated_at": "2026-11-01T22:47:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PP2 Ameliorates Renal Fibrosis by Regulating the NF-κB/COX-2 and PPARγ/UCP2 Pathway in Diabetic Mice.", "doi": "10.1155/2021/7394344", "pmid": "34580604", "authors": ["Jinying Wei", "Xinna Deng", "Yang Li", "Runmei Li", "Zhaohua Yang", "Xiuyuan Li", "Shan Song", "Yonghong Shi", "Huijun Duan", "Haijiang Wu"], "journal": "Oxidative medicine and cellular longevity", "year": 2021, "abstract": "Renal fibrosis is characterized by glomerulosclerosis and tubulointerstitial fibrosis in diabetic nephropathy (DN). We aimed to evaluate the effects of PP2 on renal fibrosis of DN. GSE33744 and GSE86300 were downloaded from the GEO database. Firstly, 839 DEGs were identified between nondiabetic and diabetic mice renal glomerular samples. COX-2 was selected to assess the effects of PP2 on renal glomerulosclerosis. In db/db mice, PP2 decreased the expression of COX-2, phosphorylated p65, and fibrotic proteins, accompanied with attenuated renal glomerulosclerosis. In cultured glomerular mesangial cells, high glucose- (HG-) induced p65 phosphorylation and COX-2 expression were attenuated by PP2 or NF-κB inhibitor PDTC. PP2, PDTC, or COX-2 inhibitor NS-398 ameliorated abnormal proliferation and expression of fibrotic proteins induced by HG. Secondly, 238 DEGs were identified between nondiabetic and diabetic mice renal cortex samples. UCP2 was selected to assess the effects of PP2 on renal tubulointerstitial fibrosis. In db/db mice, PP2 decreased the expression of PPARγ and UCP2, accompanied with attenuated renal tubulointerstitial fibrosis and EMT. In cultured proximal tubular cells, HG-induced PPARγ and UCP2 expression was inhibited by PP2 or PPARγ antagonist GW9662. PP2, GW9662, or UCP2 shRNA ameliorated HG-induced EMT. These results indicated that PP2 ameliorated renal fibrosis in diabetic mice.", "claims": [{"id": "claim-method", "statement": "Statistical analysis was performed by one-way ANOVA. Microarray gene expression profiles GSE33744 [16] and GSE86300 [17] were used to perform bioinformatic analysis, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34580604", "locator": "sections[13] \"2.11. Statistical Analysis\" paragraph 2", "quote": "Statistical analysis was performed by one-way ANOVA."}, {"asset": "source:pmid:34580604", "locator": "sections[3] \"2.1. Bioinformatic Analysis\" paragraph 2", "quote": "Microarray gene expression profiles GSE33744 [16] and GSE86300 [17] were used to perform bioinformatic analysis, respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "This study benefited from the Cancer Genome Atlas (TCGA) and GEO databases. We appreciate the data platform, and the authors uploaded their data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34580604", "locator": "sections[24] \"Data Availability\" paragraph 2", "quote": "This study benefited from the Cancer Genome Atlas (TCGA) and GEO databases. We appreciate the data platform, and the authors uploaded their data."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34580604"], "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:GSE33744"], "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:GSE33744"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34580604", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/7394344", "sha256": "sha256:1be5c4c2bf5d3a6df5d14d8ab25807e2133ada8ac2e22c201f38570ae885a504", "bytes": 46613, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/7394344", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8464423", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE33744", "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=GSE33744", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33744", "version": null, "note": "This study benefited from the Cancer Genome Atlas (TCGA) and GEO databases. We appreciate the data platform, and the authors uploaded their data.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This study benefited from the Cancer Genome Atlas (TCGA) and GEO databases. We appreciate the data platform, and the authors uploaded their data.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM833993", "GSM833994", "GSM833995", "GSM833996", "GSM833997", "GSM833998", "GSM833999", "GSM834000", "GSM834001", "GSM834002", "GSM834003", "GSM834004", "GSM834005", "GSM834006", "GSM834007", "GSM834008", "GSM834009", "GSM834010", "GSM834011", "GSM834012", "GSM834013", "GSM834014", "GSM834015", "GSM834016", "GSM834017", "GSM834018", "GSM834019", "GSM834020", "GSM834021", "GSM834022", "GSM834023", "GSM834024", "GSM834025", "GSM834026", "GSM834027", "GSM834028", "GSM834029", "GSM834030", "GSM834031"], "sample_count": 39, "group_sizes": null, "group_sizes_basis": null, "platform": "1261", "taxon": "Mus musculus", "title": "Cross-species transcriptional networks in Diabetic Glomerulopathy in mouse and man", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE86300", "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=GSE86300", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE86300", "version": null, "note": "This study benefited from the Cancer Genome Atlas (TCGA) and GEO databases. We appreciate the data platform, and the authors uploaded their data.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This study benefited from the Cancer Genome Atlas (TCGA) and GEO databases. We appreciate the data platform, and the authors uploaded their data.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2299770", "GSM2299771", "GSM2299772", "GSM2299773", "GSM2299774", "GSM2299775", "GSM2299776", "GSM2299777", "GSM2299778", "GSM2299779"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "7546", "taxon": "Mus musculus", "title": "Tissue-specific metabolic reprogramming drives nutrient flux in diabetic complications", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE33744 not downloaded", "asset:data:geo:GSE33744 licence not read", "asset:data:geo:GSE86300 not downloaded", "asset:data:geo:GSE86300 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": "reordered", "quote": "Statistical analysis was performed by one-way ANOVA. Microarray gene expression profiles GSE33744 [16] and GSE86300 [17] were used to perform bioinformatic analysis, respectively."}}], "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": ["GSE33744", "GSE86300"], "resolved_accessions": ["GSE33744", "GSE86300"], "statements": ["This study benefited from the Cancer Genome Atlas (TCGA) and GEO databases. We appreciate the data platform, and the authors uploaded their data."], "basis": "The paper names GSE33744, GSE86300 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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:34580604", "data:geo:GSE33744"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE33744"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:35:20Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 33605, "completion_tokens": 1675, "cached_tokens": 11272}}, "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:34580604", "type": "paper", "label": "pmid:34580604"}, {"id": "source:pmid:34580604", "type": "manuscript", "label": "PMID 34580604 full text"}, {"id": "data:geo:GSE33744", "type": "dataset", "label": "GEO GSE33744"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34580604", "type": "paper", "label": "pmid:34580604"}, {"id": "source:pmid:34580604", "type": "manuscript", "label": "PMID 34580604 full text"}, {"id": "data:geo:GSE33744", "type": "dataset", "label": "GEO GSE33744"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34580604", "type": "extraction", "used": ["source:pmid:34580604"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE33744", "type": "accession_resolution", "used": ["data:geo:GSE33744"], "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:34580604", "parent_hash": "sha256:72da6587635c951f64a5747605731e81397c00ede0a02be3033ad5431c5d98bf", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE33744 licence not read", "asset:data:geo:GSE33744 not downloaded", "asset:data:geo:GSE86300 licence not read", "asset:data:geo:GSE86300 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["with attenuated renal glomerulosclerosis. In cultured glomerular mesangial cells, high glucose- (H", "enal tubulointerstitial fibrosis and EMT. In cultured proximal tubular cells, HG-induced PPARγ and", "nter and stored in our laboratory. MMCs were cultured in DMEM/F12 (3 : 1) medium supplemented with 10", "ure Collection (ATCC, Manassas, VA, USA) and cultured in DMEM medium supplemented with 10% fetal bovi"], "order_basis": "paper_text_order:628", "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": ["PARγ antagonist GW9662. PP2, GW9662, or UCP2 shRNA ameliorated HG-induced EMT. These results in", "en1-UCP2 overexpression plasmid and PLV-UCP2-shRNA plasmid were purchased from Yingrun Biotechn", "ith pIRES2-ZsGreen1-UCP2 plasmid or PLV-UCP2-shRNA plasmid were performed with Lipofectamine 20"], "order_basis": "paper_text_order:1362", "id": "assay:2"}, {"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": ["ale diabetic db/db mice and nondiabetic db/m mice were purchased from the Model Animal Research Cen", "her analysis. 2.4. Cell Culture Immortalized mouse mesangial cells (MMCs) were obtained from th"], "order_basis": "paper_text_order:2947", "id": "assay:3"}, {"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": ["Statistical analysis was performed by one-way ANOVA. Microarray gene expression profiles GSE33744 [16] and GSE86300 [17] were used to perform bioinformatic analysis, respectively."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}