{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41054110", "kind": "science-record", "revision": 4, "content_hash": "sha256:d86f61ad4196325bcee79996841775b8ae89ab58b5502a313a9efc5778a68513", "created_at": "2026-11-01T20:31:06Z", "updated_at": "2026-11-01T22:57:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key mitophagy-related genes in osteomyelitis: Insights from differential gene expression and machine learning models.", "doi": "10.1097/MD.0000000000044923", "pmid": "41054110", "authors": ["Sirui Zhou", "Fan Bai", "Shiqiang Wang", "Yangyang Zhou", "Peibei Yao", "Qiang Zheng"], "journal": "Medicine", "year": 2025, "abstract": "Osteomyelitis, a severe skeletal infection, involves complex pathogenic mechanisms. Mitophagy (mitophagy) is crucial for cellular homeostasis and has been linked to various diseases, including osteomyelitis. This study explores the genetic basis of mitophagy in osteomyelitis, identifying differentially expressed genes related to mitophagy and their potential as biomarkers and therapeutic targets. Using the GSE30119 dataset from GEO, mRNA expression profiles from 49 osteomyelitis patients and 44 healthy individuals were analyzed. Differential gene expression analysis identified 2876 differentially expressed genes with a threshold of |log FC| > 0.5 and P < .05. Mitophagy-related genes were sourced from GeneCards, with 25 overlapping genes identified. Functional enrichment analyses, including gene ontology and Kyoto encyclopedia of genes and genomes, were conducted. Four machine learning models (generalized linear model, random forest, support vector machine, and extreme gradient boosting) identified 9 key genes for a diagnostic model. Gene set enrichment analysis and immune cell infiltration analysis using CIBERSORT were performed. Furthermore, RT-qPCR was performed to experimentally validate the expression patterns of the identified key genes in an inflammatory cellular model. Twenty-five intersecting genes were identified, with gene ontology and Kyoto encyclopedia of genes and genomes analyses highlighting their roles in autophagy and mitochondrial functions. The random forest model identified 9 key genes: BMP2KL, ALPK1, PGAM5, PINK1, TP53, GPC1, ITPKC, PEX3, and P2RX5, validated with an area under the receiver operating characteristic curve of 0.905. Gene set enrichment analysis indicated their involvement in metabolic and signaling pathways. Immune infiltration analysis revealed significant differences between patients and healthy individuals. RT-qPCR validation confirmed significant expression changes of the 9 key genes under inflammatory conditions, consistent with bioinformatics predictions. This study identifies key mitophagy genes and targets in osteomyelitis, providing a basis for future research and therapies.", "claims": [{"id": "claim-method", "statement": "The exploration of DEGs between normal and osteomyelitis samples was carried out using the “limma” package in R software (R Foundation for Statistical Computing, Vienna, Austria), where genes exhibiting |log FC| > 0.5 and P < .05 were identified as DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41054110", "locator": "sections[4] \"2.2. Identification of autophagy-associated differentially expressed genes (DEGs)\" paragraph 2", "quote": "The exploration of DEGs between normal and osteomyelitis samples was carried out using the “limma” package in R software (R Foundation for Statistical Computing, Vienna, Austria), where genes exhibiting |log FC| > 0.5 and P < .05 were identified as DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41054110", "locator": "sections[26] \"fn-group\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Limma-based differential-expression analysis of GSE30119 identified 2,876 differentially expressed genes in osteomyelitis versus healthy samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41054110", "locator": "sections[14] \"3.1. Identification of differentially expressed genes related to mitophagy in osteomyelitis\" paragraph 2", "quote": "We set the threshold for differential analysis at |log FC| > 0.5 and P < .05, identifying a total of 2876 DEGs (Fig. 1A, B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Limma-based differential-expression analysis of GSE30119 identified 2,876 differentially expressed genes in osteomyelitis versus healthy samples.", "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:41054110"], "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. 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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}}}