← All .science files
pmid:33411714
Extracellular vesicles released from the filarial parasite Brugia malayi downregulate the host mTOR pathway.
Alessandra Ricciardi · Sasisekhar Bennuru · Sameha Tariq · Sukhbir Kaur · Weiwei Wu · Abdel G Elkahloun · Anush Arakelyan · Jahangheer Shaik · David W Dorward · Thomas B Nutman · Roshanak Tolouei Semnani
PLoS neglected tropical diseases · 2021 doi:10.1371/journal.pntd.0008884
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
paper object · 10 fields
authors array · 11 items
claims array · 2 items
[0] object · 6 fields
[1] 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 · 1 item
data object · 3 fields
assets array · 5 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 9 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 45 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 items
[9] array · 2 items
[10] array · 2 items
[11] array · 2 items
[12] array · 2 items
[13] array · 2 items
[14] array · 2 items
[15] array · 2 items
[16] array · 2 items
[17] array · 2 items
[18] array · 2 items
[19] array · 2 items
[20] array · 2 items
[21] array · 2 items
[22] array · 2 items
[23] array · 2 items
[24] array · 2 items
[25] array · 2 items
[26] array · 2 items
[27] array · 2 items
[28] array · 2 items
[29] array · 2 items
[30] array · 2 items
[31] array · 2 items
[32] array · 2 items
[33] array · 2 items
[34] array · 2 items
[35] array · 2 items
[36] array · 2 items
[37] array · 2 items
[38] array · 2 items
[39] array · 2 items
[40] array · 2 items
[41] array · 2 items
[42] array · 2 items
[43] array · 2 items
[44] array · 2 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 6 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
gaps array · 4 items
analysis object · 4 fields
methods array · 3 items
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 1 field
data_shapes array · 1 item
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 · 1 item
capability object · 4 fields
data object · 6 fields
accessions array · 3 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 4 items
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
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 · 10 items
assays array · 5 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 · 1 item
[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 · 0 items
source_hashes object · 1 field
evidence array · 3 items
[4] object · 11 fields
required_operations array · 0 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:33411714", "kind": "science-record", "revision": 7, "content_hash": "sha256:87ec775f1f24286825d2e09966ac91043741ae6ffb5f2b7d4cac5215720b9c54", "created_at": "2026-11-01T15:41:22Z", "updated_at": "2026-11-01T22:02:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Extracellular vesicles released from the filarial parasite Brugia malayi downregulate the host mTOR pathway.", "doi": "10.1371/journal.pntd.0008884", "pmid": "33411714", "authors": ["Alessandra Ricciardi", "Sasisekhar Bennuru", "Sameha Tariq", "Sukhbir Kaur", "Weiwei Wu", "Abdel G Elkahloun", "Anush Arakelyan", "Jahangheer Shaik", "David W Dorward", "Thomas B Nutman", "Roshanak Tolouei Semnani"], "journal": "PLoS neglected tropical diseases", "year": 2021, "abstract": "We have previously shown that the microfilarial (mf) stage of Brugia malayi can inhibit the mammalian target of rapamycin (mTOR; a conserved serine/threonine kinase critical for immune regulation and cellular growth) in human dendritic cells (DC) and we have proposed that this mTOR inhibition is associated with the DC dysfunction seen in filarial infections. Extracellular vesicles (EVs) contain many proteins and nucleic acids including microRNAs (miRNAs) that might affect a variety of intracellular pathways. Thus, EVs secreted from mf may elucidate the mechanism by which the parasite is able to modulate the host immune response during infection. EVs, purified from mf of Brugia malayi and confirmed by size through nanoparticle tracking analysis, were assessed by miRNA microarrays (accession number GSE157226) and shown to be enriched (>2-fold, p-value<0.05, FDR = 0.05) for miR100, miR71, miR34, and miR7. The microarray analysis compared mf-derived EVs and mf supernatant. After confirming their presence in EVs using qPCR for these miRNA targets, web-based target predictions (using MIRPathv3, TarBAse and MicroT-CD) predicted that miR100 targeted mTOR and its downstream regulatory protein 4E-BP1. Our previous data with live parasites demonstrated that mf downregulate the phosphorylation of mTOR and its downstream effectors. Additionally, our proteomic analysis of the mf-derived EVs revealed the presence of proteins commonly found in these vesicles (data are available via ProteomeXchange with identifier PXD021844). We confirmed internalization of mf-derived EVs by human DCs and monocytes using confocal microscopy and flow cytometry, and further demonstrated through flow cytometry, that mf-derived EVs downregulate the phosphorylation of mTOR in human monocytes (THP-1 cells) to the same degree that rapamycin (a known mTOR inhibitor) does. Our data collectively suggest that mf release EVs that interact with host cells, such as DC, to modulate host responses.", "claims": [{"id": "claim-method", "statement": "For analysis of flow cytometry data, Wilcoxon test was used in order to compare nonparametric paired data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33411714", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "For analysis of flow cytometry data, Wilcoxon test was used in order to compare nonparametric paired data."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Relevant data are within the manuscript. In addition, the mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD021844 and 10.6019/PXD021844. The microarray data have been uploaded to the Gene Expression Omnibus at NCBI with the accession number GSE157226.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33411714", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "Relevant data are within the manuscript. In addition, the mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD021844 and 10.6019/PXD021844. The microarray data have been uploaded to the Gene Expression Omnibus at NCBI with the accession number GSE157226."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:33411714"], "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:GSE157226"], "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:group_comparison_wilcoxon", "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:GSE157226"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33411714", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pntd.0008884", "sha256": "sha256:5eaa3650b38dab05b887a1b70409c8de7d69d378ed576776da8adacadd0af54a", "bytes": 55012, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pntd.0008884", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7790274", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE157226", "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=GSE157226", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE157226", "version": null, "note": "Relevant data are within the manuscript. In addition, the mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD021844 and 10.6019/PXD021844. The microarray data have been uploaded to the Gene Expression Omnibus at NCBI with the accession number GSE157226.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Relevant data are within the manuscript. In addition, the mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD021844 and 10.6019/PXD021844. The microarray data have been uploaded to the Gene Expression Omnibus at NCBI with the accession number GSE157226.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4759456", "GSM4759457", "GSM4759458", "GSM4759459", "GSM4759460", "GSM4759461", "GSM4759462", "GSM4759463", "GSM4759464"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "19117", "taxon": "synthetic construct; Brugia malayi", "title": "Microarray analysis of Brugia malayi microfilariae-derived extracellular vesicles (Evs) and supernatants", "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:PXD021844", "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=PXD021844", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD021844", "version": null, "note": "Relevant data are within the manuscript. In addition, the mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD021844 and 10.6019/PXD021844. The microarray data have been uploaded to the Gene Expression Omnibus at NCBI with the accession number GSE157226.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Relevant data are within the manuscript. In addition, the mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD021844 and 10.6019/PXD021844. The microarray data have been uploaded to the Gene Expression Omnibus at NCBI with the accession number GSE157226.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic analysis of Brugia malayi microfilaria-derived extracellular vesicles", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33411714:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:80425b4da272642b22ca7ae7eddcbff5d3e37095a463f79d4351d1be35c521fc", "bytes": 2105, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#pntd.0008884.t001", "version": null, "note": "Proteins present in all EV preparations analyzed.", "structure": {"pmcid": "PMC7790274", "section_index": 14, "section_title": "Mf release exosome like vesicles", "row_count": 45, "column_count": 2}, "table": {"label": "Table 1", "caption": "Proteins present in all EV preparations analyzed.", "rows": [["Accession Number", "Protein Description"], ["P90689|ACT_BRUMA", "Actin"], ["A0A0K0JJB8_BRUMA", "Actin"], ["A0A1P6C3D2_BRUMA", "Bm5086 (Actin)"], ["A0A0H5SER1_BRUMA", "Bm8524 isoform a (Actin)"], ["P27541|HSP70_BRUMA", "Heat shock 70 kDa protein"], ["A0A0K0JHW8_BRUMA", "Elongation factor 1-alpha"], ["A0A0H5S3P5_BRUMA", "Phosphoglycerate kinase"], ["A0A0H5S7Y7_BRUMA", "BMA-DAF-21 (HSP-90)"], ["A0A0K0K0E4_BRUMA", "Histone H2A"], ["A0A0K0J213_BRUMA", "Bm1715 (vWA)"], ["A0A0K0IZ73_BRUMA", "ATP synthase subunit alpha"], ["A0A0J9XXG7_BRUMA", "Glyceraldehyde-3-phosphate dehydrogenase"], ["A0A1P6C609_BRUMA", "BMA-ENPL-1 isoform a"], ["A0A0K0IZQ6_BRUMA", "Bm13965 (bma-enol-1)"], ["A0A0K0IZ71_BRUMA", "ATP synthase subunit beta"], ["A0A0I9R327_BRUMA", "Eukaryotic translation initiation factor 5A"], ["A0A1P6C045_BRUMA", "Histone H4"], ["A0A0K0IYR7_BRUMA", "BMA-TUFM-1"], ["A0A0K0IRL6_BRUMA", "Bm8805"], ["A0A158Q277_BRUMA", "Uncharacterized protein"], ["A0A158Q275_BRUMA", "Uncharacterized protein"], ["A0A158Q274_BRUMA", "Uncharacterized protein"], ["A0A158Q276_BRUMA", "Uncharacterized protein"], ["A0A0K0IYG8_BRUMA", "Bm13661 (HSP-70)"], ["A0A0K0J5L7_BRUMA", "Bm2363 isoform e"], ["A0A0K0J5L8_BRUMA", "Bm2363 isoform e"], ["A0A0K0J5L6_BRUMA", "Bm2363 isoform e"], ["A0A0K0JSW0_BRUMA", "Uncharacterized protein"], ["A0A0K0JD75_BRUMA", "Histone H3"], ["A0A0K0JRX5_BRUMA", "Uncharacterized protein"], ["A0A0K0JJA2_BRUMA", "BMA-TAG-189"], ["A0A0R3REA3_BRUMA", "Uncharacterized protein"], ["A0A0R3REA2_BRUMA", "Uncharacterized protein"], ["A0A158T1L3_BRUMA", "BMA-NMTN-1 isoform a"], ["A0A0K0JED9_BRUMA", "Bm4375 isoform a"], ["A0A0J9Y2D8_BRUMA", "Bm4375 isoform a"], ["A0A0K0JED8_BRUMA", "Bm4375 isoform a"], ["A0A0K0JED5_BRUMA", "Bm4375 isoform a"], ["A0A0H5SBL8_BRUMA", "Bm4375 isoform a"], ["A0A158PTJ7_BRUMA", "Bm6177 isoform f"], ["A0A0K0ISD1_BRUMA", "Uncharacterized protein"], ["A0A0J9XXN3_BRUMA", "Bm7266"], ["A0A0K0IVY8_BRUMA", "Bm12835"], ["A0A0I9NBR2_BRUMA", "Bm12804"]], "row_count": 45, "column_count": 2, "numeric_cells": 42, "header_rows": 1, "locator": "section[14]/table-wrap[1]#pntd.0008884.t001"}}, {"id": "asset:table:pmid:33411714:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e738e7a5d7e3b0513260e9c0595d0eaafa2ce06dd2b198430ee921ae799b0337", "bytes": 412, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#pntd.0008884.t002", "version": null, "note": "EV miRNAs with potential target genes in the mTOR pathway.", "structure": {"pmcid": "PMC7790274", "section_index": 16, "section_title": "Mf-derived EVs have a distinctive nucleic acid profile", "row_count": 6, "column_count": 2}, "table": {"label": "Table 2", "caption": "EV miRNAs with potential target genes in the mTOR pathway.", "rows": [["miRNAs present in mf-derived EVs", "Target genes in mTOR pathway"], ["mir-100mir-99amir-7", "mTOR"], ["mir-34amir-9", "Ras"], ["mir-31mir-4299mir-92a", "PI3K"], ["Let-7", "eIF-4E"], ["mir-71", "PDK1"]], "row_count": 6, "column_count": 2, "numeric_cells": 6, "header_rows": 1, "locator": "section[16]/table-wrap[1]#pntd.0008884.t002"}}], "gaps": ["asset:data:geo:GSE157226 not downloaded", "asset:data:geo:GSE157226 licence not read", "asset:data:geo:PXD021844 not downloaded", "asset:data:geo:PXD021844 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For analysis of flow cytometry data, Wilcoxon test was used in order to compare nonparametric paired data."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fdr_threshold": "nt and using Limma with FDR of 0"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "Limma"}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "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": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["PXD021844", "10.6019/PXD021844", "GSE157226"], "resolved_accessions": ["PXD021844", "GSE157226"], "statements": ["Relevant data are within the manuscript. In addition, the mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD021844 and 10.6019/PXD021844. The microarray data have been uploaded to the Gene Expression Omnibus at NCBI with the accession number GSE157226."], "basis": "The paper names PXD021844, GSE157226 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:33411714", "data:geo:GSE157226", "asset:table:pmid:33411714:1", "asset:table:pmid:33411714:2"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE157226"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:00Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 41923, "completion_tokens": 1485, "cached_tokens": 776}}, "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:33411714", "type": "paper", "label": "pmid:33411714"}, {"id": "source:pmid:33411714", "type": "manuscript", "label": "PMID 33411714 full text"}, {"id": "data:geo:GSE157226", "type": "dataset", "label": "GEO GSE157226"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33411714", "type": "paper", "label": "pmid:33411714"}, {"id": "source:pmid:33411714", "type": "manuscript", "label": "PMID 33411714 full text"}, {"id": "data:geo:GSE157226", "type": "dataset", "label": "GEO GSE157226"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33411714", "type": "extraction", "used": ["source:pmid:33411714"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE157226", "type": "accession_resolution", "used": ["data:geo:GSE157226"], "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:33411714", "parent_hash": "sha256:62c97024f2f934751f64e6f9a42880fe5c6dd5c248159ca100bfa8a9f995e0a0", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE157226 licence not read", "asset:data:geo:GSE157226 not downloaded", "asset:data:geo:PXD021844 licence not read", "asset:data:geo:PXD021844 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": [".05) for miR100, miR71, miR34, and miR7. The microarray analysis compared mf-derived EVs and mf supe", "Methods Microarray analysis of miRNA Mf supernatant and EV miRN", "also grouped them all as unique miRNAs. The microarray data have been uploaded to the Gene Expressi", "h the FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix-ThermoFisher Scientific, cat#901911, Walthma"], "order_basis": "paper_text_order:984", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["After confirming their presence in EVs using qPCR for these miRNA targets, web-based target pr"], "order_basis": "paper_text_order:1093", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_imaging", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["derived EVs by human DCs and monocytes using confocal microscopy and flow cytometry, and further demonstrated", "Vs by human DCs and monocytes using confocal microscopy and flow cytometry, and further demonstrated"], "order_basis": "paper_text_order:1679", "id": "assay:3"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["and monocytes using confocal microscopy and flow cytometry, and further demonstrated through flow cytom", "cytometry, and further demonstrated through flow cytometry, that mf-derived EVs downregulate the phosph", "argets. Statistical analysis For analysis of flow cytometry data, Wilcoxon test was used in order to com"], "order_basis": "paper_text_order:1704", "id": "assay:4"}, {"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": ["For analysis of flow cytometry data, Wilcoxon test was used in order to compare nonparametric paired data."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}