{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32328182", "kind": "science-record", "revision": 7, "content_hash": "sha256:9deb4b98879b622fef4a7d76ca631ea3439761214f18e5d35b6b16b22db6e6ac", "created_at": "2026-11-01T15:41:00Z", "updated_at": "2026-11-01T21:23:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "MiR-891a-5p as a prognostic marker and therapeutic target for hormone receptor-positive breast cancer.", "doi": "10.7150/jca.40750", "pmid": "32328182", "authors": ["Zhiqiang Zhang", "Lu Xu", "Lijie He", "Jin Wang", "Xiaonan Shi", "Zhi Li", "Sha Shi", "Kezuo Hou", "Yuee Teng", "Xiujuan Qu"], "journal": "Journal of Cancer", "year": 2020, "abstract": "Background: Breast cancer is one of the most frequent malignant tumors worldwide, with 1.67 million newly-diagnosed cases and 522,000 deaths each year. Therefore, seeking the novel biomarkers and therapeutic targets that contribute to postoperative recurrence and metastasis in patients with breast cancer is emerging and facilitates the development of innovative therapeutics. Methods: Retrieving the dataset of patients with hormone receptor (HR)-positive breast cancers from Gene Expression Omnibus (GEO) and collecting the data from the patients with HR-positive breast cancers enrolled in the First Affiliated Hospital of China Medical University are so as to identify the miRNAs associated with metastasis and distant metastasis-free survival (DMFS). Then MTT and Transwell migration assays were used to validate the effect of miRNAs on cell proliferation and migration of estrogen receptor-positive breast cancer T47D and MCF7 cells in vitro, respectively. Results: From GSE59829 dataset, the miRNA expression levels of miR-891a-5p, miR-383-5p and miR-1295a were significantly downregulated while the levels of miR-128-3p, miR-661 and miR-296-3p were significantly upregulated in breast cancers from patients with metastasis as compared to the matched non-metastatic group. Moreover, low expression levels of miR-891a-5p, miR-383-5p and miR-1295a or high expression levels of miR-128-3p, miR-661 and miR-296-3p were respectively associated with low DMFS in patients with breast cancer. Our clinical cohort study supported that the levels of miR-891a-5p, miR-383-5p and miR-1295a were significantly lower in breast cancers from the metastasis group when compared with non-metastatic group. However, there is no significant difference with regard to the levels of miR-128-3p, miR-661 and miR-296-3p in breast cancer between these two groups. Moreover, low expression levels of miR-891a-5p and miR-383-5p but not miR-1295a in breast cancer were significantly associated with low DMFS in patients, implying that the expression of miR-891a-5p and miR-383-5p were the potential prognosis markers for metastatic human breast cancers. Further investigation disclosed that miR-891a-5p but not miR-383-5p restrained both proliferation and migration of T47D and MCF7 cells. In silico analysis of miRNAs target gene through online computational algorithms revealed that A Disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) is the downstream target for miR-891a-5p. Further study confirmed that miR-891a-5p impeded ADAM10 expression by directly binding to its 3'UTR, leading to the inhibition of breast cancer cells proliferation and migration. Moreover, silencing ADAM10 inhibited T47D and MCF7 cells growth and migration. Conclusion: miR-891a-5p is the vital prognostic marker for HR-positive breast cancer. In addition, miR-891a-5p and miR-383-5p are the potential targets for HR-positive breast cancer therapeutics.", "claims": [{"id": "claim-method", "statement": "T-test was used for comparison between test groups and P < 0.05 was considered as statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32328182", "locator": "sections[15] \"Statistics\" paragraph 2", "quote": "T-test was used for comparison between test groups and P < 0.05 was considered as statistical significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original data were retrieved from the GEO database of NCBI (www.ncbi.nlm.nih.gov/geo), and the access number is GSE59829. A total of 1146 miRNAs were detected on the platform (>97%, includes all of the miRNAs in microBase 12.0), and the access number was GPL8179. Consequently, the data from 54 cases of patients with T1N0M0, ESR1(+)/ERBB2(-) breast cancer were used in this study. Among them, 21 patients had distant metastasis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32328182", "locator": "sections[3] \"Retrieval of the miRNAs expression profile\" paragraph 3", "quote": "The original data were retrieved from the GEO database of NCBI (www.ncbi.nlm.nih.gov/geo), and the access number is GSE59829."}, {"asset": "source:pmid:32328182", "locator": "sections[3] \"Retrieval of the miRNAs expression profile\" paragraph 3", "quote": "A total of 1146 miRNAs were detected on the platform (>97%, includes all of the miRNAs in microBase 12.0), and the access number was GPL8179."}, {"asset": "source:pmid:32328182", "locator": "sections[4] \"Analysis of miRNAs expression profile\" paragraph 2", "quote": "Consequently, the data from 54 cases of patients with T1N0M0, ESR1(+)/ERBB2(-) breast cancer were used in this study."}, {"asset": "source:pmid:32328182", "locator": "sections[4] \"Analysis of miRNAs expression profile\" paragraph 2", "quote": "Among them, 21 patients had distant metastasis."}], "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:32328182"], "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:GSE59829"], "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:GSE59829"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32328182", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/jca.40750", "sha256": "sha256:18f6baaf26a9c2e2aa8b690ab666b771fe66507261c40ddfab242ac7f151cc5a", "bytes": 45793, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/jca.40750", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7171503", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE59829", "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=GSE59829", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59829", "version": null, "note": "The original data were retrieved from the GEO database of NCBI (www.ncbi.nlm.nih.gov/geo), and the access number is GSE59829. A total of 1146 miRNAs were detected on the platform (>97%, includes all of the miRNAs in microBase 12.0), and the access number was GPL8179. Consequently, the data from 54 cases of patients with T1N0M0, ESR1(+)/ERBB2(-) breast cancer were used in this study. Among them, 21 patients had distant metastasis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original data were retrieved from the GEO database of NCBI (www.ncbi.nlm.nih.gov/geo), and the access number is GSE59829. A total of 1146 miRNAs were detected on the platform (>97%, includes all of the miRNAs in microBase 12.0), and the access number was GPL8179. Consequently, the data from 54 cases of patients with T1N0M0, ESR1(+)/ERBB2(-) breast cancer were used in this study. 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independent subtype-specific prognostic marker in breast cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32328182:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bdd8643aa2e5735c0de9e2fd2ce22731cab8853984d86a6840ce2b7c63f1b7cc", "bytes": 1210, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#T1", "version": null, "note": "The detailed information and characteristics of breast tumors collected from patients the First Affiliated Hospital of China Medical University", "structure": {"pmcid": "PMC7171503", "section_index": 18, "section_title": "miR-891a-5p and miR-383-5p as prognosis markers for metastatic human breast cancers", "row_count": 23, "column_count": 4}, "table": {"label": "Table 1", "caption": "The detailed information and characteristics of breast tumors collected from patients the First Affiliated Hospital of China Medical University", "rows": [["Variables", "Metastasis (n=28)", "Without metastasis (n=34)", "p"], ["Age(years) , n(%)", "", "", "0.816"], ["≤ 50", "19 (67.86)", "24 (70.59)", ""], [">50", "9 (32.14)", "10 (29.41)", ""], ["T stage, n(%)", "", "", "0.779"], ["T1", "13 (46.4)", "17 (50.0)", ""], ["T2", "15 (53.6)", "17 (50.0)", ""], ["Adjuvant therapy, n (%)", "", "", "0.705"], ["Chemotherapy", "19 (67.9)", "20 (58.8)", ""], ["Hormone therapy", "27 (96.4)", "34 (100.0)", ""], ["Molecular subtyping,n(%)", "", "", "0.424"], ["Luminal A", "8 (28.6)", "13 (38.24)", ""], ["Luminal B", "20 (71.4)", "21 (61.76)", ""], ["Histotype ,n(%)", "", "", "0.737"], ["IDC", "23 (82.1)", "29 (85.29)", ""], ["rests (ILC, DCIS-MI, mucinous carcinoma)", "5 (17.9)", "5 (14.71)", ""], ["Metastatic sites, n(%)", "", "", "NA"], ["Lung metastasis", "9", "NA", ""], ["osseous metastasis", "12", "NA", ""], ["hepatic metastases", "7", "NA", ""], ["Follow-up time (months)", "", "", "<0.001"], ["Min-Max", "6-86", "59-131", ""], ["Median", "46", "81", ""]], "row_count": 23, "column_count": 4, "numeric_cells": 37, "header_rows": 1, "locator": "section[18]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:GSE59829 not downloaded", "asset:data:geo:GSE59829 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "T-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "T-test was used for comparison between test groups and P < 0.05 was considered as statistical significance."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32328182", "data:geo:GSE59829", "asset:table:pmid:32328182:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE59829"]}, "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": "2026-10-31T18:19:26Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 38176, "completion_tokens": 1492, "cached_tokens": 784}}, "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:32328182", "type": "paper", "label": "pmid:32328182"}, {"id": "source:pmid:32328182", "type": "manuscript", "label": "PMID 32328182 full text"}, {"id": "data:geo:GSE59829", "type": "dataset", "label": "GEO GSE59829"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32328182", "type": "paper", "label": "pmid:32328182"}, {"id": "source:pmid:32328182", "type": "manuscript", "label": "PMID 32328182 full text"}, {"id": "data:geo:GSE59829", "type": "dataset", "label": "GEO GSE59829"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32328182", "type": "extraction", "used": ["source:pmid:32328182"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE59829", "type": "accession_resolution", "used": ["data:geo:GSE59829"], "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:32328182", "parent_hash": "sha256:96543db848c46f0f240554b2e48ab50152380c90da2355cd1956ab919a71b626", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE59829 licence not read", "asset:data:geo:GSE59829 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["istant metastasis-free survival (DMFS). Then MTT and Transwell migration assays were used to"], "order_basis": "paper_text_order:820", "id": "assay:1"}, {"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": ["gen receptor-positive breast cancer T47D and MCF7 cells in vitro, respectively. Results: From", "both proliferation and migration of T47D and MCF7 cells. In silico analysis of miRNAs target g", "oreover, silencing ADAM10 inhibited T47D and MCF7 cells growth and migration. Conclusion: miR-", "CAAUCACCUUCUGAUCU-3'). 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Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. 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At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. 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Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}