{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37476188", "kind": "science-record", "revision": 4, "content_hash": "sha256:d4c39ba19cbbb2243139187e9c29ea603169d01e585c3178465267883c1b3946", "created_at": "2026-11-01T19:02:14Z", "updated_at": "2026-11-01T22:52:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "High Expression of Microtubule-associated Protein TBCB Predicts Adverse Outcome and Immunosuppression in Acute Myeloid Leukemia.", "doi": "10.7150/jca.84215", "pmid": "37476188", "authors": ["Bichen Wang", "Wenjun Wang", "Qiaoli Li", "Tengxiao Guo", "Shuang Yang", "Jun Shi", "Weiping Yuan", "Yajing Chu"], "journal": "Journal of Cancer", "year": 2023, "abstract": "Acute myeloid leukemia (AML) is a devastating blood cancer with high heterogeneity and ill-fated outcome. Despite numerous advances in AML treatment, the prognosis remains poor for a significant proportion of patients. Consequently, it is necessary to accurately and comprehensively identify biomarkers as soon as possible to enhance the efficacy of diagnosis, prognosis and treatment of AML. In this study, we aimed to identify prognostic markers of AML by analyzing the cohorts from TCGA-LAML database and GEO microarray datasets. Interestingly, the transcriptional level of microtubule-associated protein TBCB in AML patients was noticeably increased when compared with normal individuals, and this was verified in two independent cohorts (GSE9476 and GSE13159) and with our AML patients. Furthermore, univariate and multivariate regression analysis revealed that high TBCB expression was an independent poor prognostic factor for AML. GO and GSEA enrichment analysis hinted that immune-related signaling pathways were enriched in up-regulated DEGs between two populations separated by the median expression level of TBCB. By constructing a protein-protein interaction network, we obtained six hub genes, all of which are immune-related molecules, and their expression levels were positively linked to that of TBCB. In addition, the high expression of three hub genes was significantly associated with a poor prognosis in AML. Moreover, we found that the tumor microenvironment in AML with high TBCB expression tended to be infiltrated by NK cells, especially CD56bright NK cells. The transcriptional levels of NK cell inhibitory receptors and their ligands were positively related to that of TBCB, and their high expression levels also predicted poor prognosis in AML. Notably, we found that the down-regulation of TBCB suppressed cell proliferation in AML cell lines by enhancing the apoptosis and cell cycle arrest. Finally, drug sensitivity prediction illustrated that cells with high TBCB expression were more responsive to ATRA and midostaurin but resistant to cytarabine, dasatinib, and imatinib. In conclusion, our findings shed light on the feasibility of TBCB as a potential predictor of poor outcome and to be an alternative target of treatment in AML.", "claims": [{"id": "claim-method", "statement": "The overall survival (OS) was conducted by Kaplan-Meier, and univariate and multivariate Cox regression were used to determine the significance of prognostic factors (p < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37476188", "locator": "sections[18] \"Statistical analysis\" paragraph 2", "quote": "The overall survival (OS) was conducted by Kaplan-Meier, and univariate and multivariate Cox regression were used to determine the significance of prognostic factors (p < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used in this study were obtained from the public databases. Details can be found in Material and methods.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37476188", "locator": "sections[33] \"Data availability statement\" paragraph 2", "quote": "The datasets used in this study were obtained from the public databases. Details can be found in Material and methods."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Furthermore, univariate and multivariate regression analysis revealed that high TBCB expression was an independent poor prognostic factor for AML.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37476188", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Furthermore, univariate and multivariate regression analysis revealed that high TBCB expression was an independent poor prognostic factor for AML."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Furthermore, univariate and multivariate regression analysis revealed that high TBCB expression was an independent poor prognostic factor for AML.", "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:37476188"], "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:GSE13159"], "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:GSE13159"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37476188", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/jca.84215", "sha256": "sha256:9b83064b14388eb3dcb7dddf6be05ea45548d41eed068c0dc3c4ffb67f69f469", "bytes": 58409, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/jca.84215", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10355208", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13159", "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=GSE13159", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13159", "version": null, "note": "The datasets used in this study were obtained from the public databases. Details can be found in Material and methods.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study were obtained from the public databases. Details can be found in Material and methods.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM329407", "GSM329408", "GSM329409", "GSM329410", "GSM329411", "GSM329412", "GSM329413", "GSM329414", "GSM329415", "GSM329416", "GSM329417", "GSM329418", "GSM329419", "GSM329420", "GSM329421", "GSM329422", "GSM329423", "GSM329424", "GSM329425", "GSM329426", "GSM329427", "GSM329428", "GSM329429", "GSM329430", "GSM329431", "GSM329432", "GSM329433", "GSM329434", "GSM329435", "GSM329436", "GSM329437", "GSM329438", "GSM329439", "GSM329440", "GSM329441", "GSM329442", "GSM329443", "GSM329444", "GSM329445", "GSM329446", "GSM329447", "GSM329448", "GSM329449", "GSM329450", "GSM329451", "GSM329452", "GSM329453", "GSM329454", "GSM329455", "GSM329456", "GSM329457", "GSM329458", "GSM329459", "GSM329460", "GSM329461", "GSM329462", "GSM329463", "GSM329464", "GSM329465", "GSM329466", "GSM329467", "GSM329468", "GSM329469", "GSM329470", "GSM329471", "GSM329472", "GSM329473", 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"GSM330551", "GSM330552", "GSM330553", "GSM330554", "GSM330555", "GSM330556", "GSM330557", "GSM330558", "GSM330559", "GSM330560", "GSM330561", "GSM330562", "GSM330563", "GSM330564", "GSM330565", "GSM330566", "GSM330567", "GSM330568", "GSM330569", "GSM330570", "GSM330571", "GSM330572", "GSM330573", "GSM330574", "GSM330575", "GSM330576", "GSM330577", "GSM330578", "GSM330579", "GSM330580", "GSM330581", "GSM330582", "GSM330583", "GSM330584", "GSM330585", "GSM330586", "GSM330587", "GSM330588", "GSM330589", "GSM330590", "GSM330591", "GSM330592", "GSM330593", "GSM330594", "GSM330595", "GSM330596", "GSM330597", "GSM330598", "GSM330599", "GSM330600", "GSM330601", "GSM330602", "GSM330603", "GSM330604", "GSM330605", "GSM330606", "GSM330607", "GSM330608", "GSM330609", "GSM330610", "GSM330611", "GSM330612", "GSM330613", "GSM330614", "GSM330615", "GSM330616", "GSM330617", "GSM330618", "GSM330619", "GSM330620", "GSM330621", "GSM330622", "GSM330623", "GSM330624", "GSM330625", "GSM330626", "GSM330627", "GSM330628", "GSM330629", "GSM330630", "GSM330631", "GSM330632", "GSM330633", "GSM330634", "GSM330635", "GSM330636", "GSM330637", "GSM330638", "GSM330639", "GSM330640", "GSM330641", "GSM330642", "GSM330643", "GSM330644", "GSM330645", "GSM330646", "GSM330647", "GSM330648", "GSM330649", "GSM330650", "GSM330651", "GSM330652", "GSM330653", "GSM330654", "GSM330655", "GSM330656", "GSM330657", "GSM330658", "GSM330659", "GSM330660", "GSM330661", "GSM330662", "GSM330663", "GSM330664", "GSM330665", "GSM330666", "GSM330667", "GSM330668", "GSM330669", "GSM330670", "GSM330671", "GSM330672", "GSM330673", "GSM330674", "GSM330675", "GSM330676", "GSM330677", "GSM330678", "GSM330679", "GSM330680", "GSM330681", "GSM330682", "GSM330683", "GSM330684", "GSM330685", "GSM330686", "GSM330687", "GSM330688", "GSM330689", "GSM330690", "GSM330691", "GSM330692", "GSM330693", "GSM330694", "GSM330695", "GSM330696", "GSM330697", "GSM330698", "GSM330699", "GSM330700", "GSM330701", "GSM330702", "GSM330703", "GSM330704", "GSM330705", "GSM330706", "GSM330707", "GSM330708", "GSM330709", "GSM330710", "GSM330711", "GSM330712", "GSM330713", "GSM330714", "GSM330715", "GSM330716", "GSM330717", "GSM330718", "GSM330719", "GSM330720", "GSM330721", "GSM330722", "GSM330723", "GSM330724", "GSM330725", "GSM330726", "GSM330727", "GSM330728", "GSM330729", "GSM330730", "GSM330731", "GSM330732", "GSM330733", "GSM330734", "GSM330735", "GSM330736", "GSM330737", "GSM330738", "GSM330739", "GSM330740", "GSM330741", "GSM330742", "GSM330743", "GSM330744", "GSM330745", "GSM330746", "GSM330747", "GSM330748", "GSM330749", "GSM330750", "GSM330751", "GSM330752", "GSM330753", "GSM330754", "GSM330755", "GSM330756", "GSM330757", "GSM330758", "GSM330759", "GSM330760", "GSM330761", "GSM330762", "GSM330763", "GSM330764", "GSM330765", "GSM330766", "GSM330767", "GSM330768", "GSM330769", "GSM330770", "GSM330771", "GSM330772", "GSM330773", "GSM330774", "GSM330775", "GSM330776", "GSM330777", "GSM330778", "GSM330779", "GSM330780", "GSM330781", "GSM330782", "GSM330783", "GSM330784", "GSM330785", "GSM330786", "GSM330787", "GSM330788", "GSM330789", "GSM330790", "GSM330791", "GSM330792", "GSM330793", "GSM330794", "GSM330795", "GSM330796", "GSM330797", "GSM330798", "GSM330799", "GSM330800", "GSM330801", "GSM330802", "GSM330803", "GSM330804", "GSM330805", "GSM330806", "GSM330807", "GSM330808", "GSM330809", "GSM330810", "GSM330811", "GSM330812", "GSM330813", "GSM330814", "GSM330815", "GSM330816", "GSM330817", "GSM330818", "GSM330819", "GSM330820", "GSM330821", "GSM330822", "GSM330823", "GSM330824", "GSM330825", "GSM330826", "GSM330827", "GSM330828", "GSM330829", "GSM330830", "GSM330831", "GSM330832", "GSM330833", "GSM330834", "GSM330835", "GSM330836", "GSM330837", "GSM330838", "GSM330839", "GSM330840", "GSM330841", "GSM330842", "GSM330843", "GSM330844", "GSM330845", "GSM330846", "GSM330847", "GSM330848", "GSM330849", "GSM330850", "GSM330851", "GSM330852", "GSM330853", "GSM330854", "GSM330855", "GSM330856", "GSM330857", "GSM330858", "GSM330859", "GSM330860", "GSM330861", "GSM330862", "GSM330863", "GSM330864", "GSM330865", "GSM330866", "GSM330867", "GSM330868", "GSM330869", "GSM330870", "GSM330871", "GSM330872", "GSM330873", "GSM330874", "GSM330875", "GSM330876", "GSM330877", "GSM330878", "GSM330879", "GSM330880", "GSM330881", "GSM330882", "GSM330883", "GSM330884", "GSM330885", "GSM330886", "GSM330887", "GSM330888", "GSM330889", "GSM330890", "GSM330891", "GSM330892", "GSM330893", "GSM330894", "GSM330895", "GSM330896", "GSM330897", "GSM330898", "GSM330899", "GSM330900", "GSM330901", "GSM330902", "GSM330903", "GSM330904", "GSM330905", "GSM330906", "GSM330907", "GSM330908", "GSM330909", "GSM330910", "GSM330911", "GSM330912", "GSM330913", "GSM330914", "GSM330915", "GSM330916", "GSM330917", "GSM330918", "GSM330919", "GSM330920", "GSM330921", "GSM330922", "GSM330923", "GSM330924", "GSM330925", "GSM330926", "GSM330927", "GSM330928", "GSM330929", "GSM330930", "GSM330931", "GSM330932", "GSM330933", "GSM330934", "GSM330935", "GSM330936", "GSM330937", "GSM330938", "GSM330939", "GSM330940", "GSM330941", "GSM330942", "GSM330943", "GSM330944", "GSM330945", "GSM330946", "GSM330947", "GSM330948", "GSM330949", "GSM330950", "GSM330951", "GSM330952", "GSM330953", "GSM330954", "GSM330955", "GSM330956", "GSM330957", "GSM330958", "GSM330959", "GSM330960", "GSM330961", "GSM330962", "GSM330963", "GSM330964", "GSM330965", "GSM330966", "GSM330967", "GSM330968", "GSM330969", "GSM330970", "GSM330971", "GSM330972", "GSM330973", "GSM330974", "GSM330975", "GSM330976", "GSM330977", "GSM330978", "GSM330979", "GSM330980", "GSM330981", "GSM330982", "GSM330983", "GSM330984", "GSM330985", "GSM330986", "GSM330987", "GSM330988", "GSM330989", "GSM330990", "GSM330991", "GSM330992", "GSM330993", "GSM330994", "GSM330995", "GSM330996", "GSM330997", "GSM330998", "GSM330999", "GSM331000", "GSM331001", "GSM331002", "GSM331003", "GSM331004", "GSM331005", "GSM331006", "GSM331007", "GSM331008", "GSM331009", "GSM331010", "GSM331011", "GSM331012", "GSM331013", "GSM331014", "GSM331015", "GSM331016", "GSM331017", "GSM331018", "GSM331019", "GSM331020", "GSM331021", "GSM331022", "GSM331023", "GSM331024", "GSM331025", "GSM331026", "GSM331027", "GSM331028", "GSM331029", "GSM331030", "GSM331031", "GSM331032", "GSM331033", "GSM331034", "GSM331035", "GSM331036", "GSM331037", "GSM331038", "GSM331039", "GSM331040", "GSM331041", "GSM331042", "GSM331043", "GSM331044", "GSM331045", "GSM331046", "GSM331047", "GSM331048", "GSM331049", "GSM331050", "GSM331051", "GSM331052", "GSM331053", "GSM331054", "GSM331055", "GSM331056", "GSM331057", "GSM331058", "GSM331059", "GSM331060", "GSM331061", "GSM331062", "GSM331063", "GSM331064", "GSM331065", "GSM331066", "GSM331067", "GSM331068", "GSM331069", "GSM331070", "GSM331071", "GSM331072", "GSM331073", "GSM331074", "GSM331075", "GSM331076", "GSM331077", "GSM331078", "GSM331079", "GSM331080", "GSM331081", "GSM331082", "GSM331083", "GSM331084", "GSM331085", "GSM331086", "GSM331087", "GSM331088", "GSM331089", "GSM331090", "GSM331091", "GSM331092", "GSM331093", "GSM331094", "GSM331095", "GSM331096", "GSM331097", "GSM331098", "GSM331099", "GSM331100", "GSM331101", "GSM331102", "GSM331103", "GSM331104", "GSM331105", "GSM331106", "GSM331107", "GSM331108", "GSM331109", "GSM331110", "GSM331111", "GSM331112", "GSM331113", "GSM331114", "GSM331115", "GSM331116", "GSM331117", "GSM331118", "GSM331119", "GSM331120", "GSM331121", "GSM331122", "GSM331123", "GSM331124", "GSM331125", "GSM331126", "GSM331127", "GSM331128", "GSM331129", "GSM331130", "GSM331131", "GSM331132", "GSM331133", "GSM331134", "GSM331135", "GSM331136", "GSM331137", "GSM331138", "GSM331139", "GSM331140", "GSM331141", "GSM331142", "GSM331143", "GSM331144", "GSM331145", "GSM331146", "GSM331147", "GSM331148", "GSM331149", "GSM331150", "GSM331151", "GSM331152", "GSM331153", "GSM331154", "GSM331155", "GSM331156", "GSM331157", "GSM331158", "GSM331159", "GSM331160", "GSM331161", "GSM331162", "GSM331163", "GSM331164", "GSM331165", "GSM331166", "GSM331167", "GSM331168", "GSM331169", "GSM331170", "GSM331171", "GSM331172", "GSM331173", "GSM331174", "GSM331175", "GSM331176", "GSM331177", "GSM331178", "GSM331179", "GSM331180", "GSM331181", "GSM331182", "GSM331183", "GSM331184", "GSM331185", "GSM331186", "GSM331187", "GSM331188", "GSM331189", "GSM331190", "GSM331191", "GSM331192", "GSM331193", "GSM331194", "GSM331195", "GSM331196", "GSM331197", "GSM331198", "GSM331199", "GSM331200", "GSM331201", "GSM331202", "GSM331203", "GSM331204", "GSM331205", "GSM331206", "GSM331207", "GSM331208", "GSM331209", "GSM331210", "GSM331211", "GSM331212", "GSM331213", "GSM331214", "GSM331215", "GSM331216", "GSM331217", "GSM331218", "GSM331219", "GSM331220", "GSM331221", "GSM331222", "GSM331223", "GSM331224", "GSM331225", "GSM331226", "GSM331227", "GSM331228", "GSM331229", "GSM331230", "GSM331231", "GSM331232", "GSM331233", "GSM331234", "GSM331235", "GSM331236", "GSM331237", "GSM331238", "GSM331239", "GSM331240", "GSM331241", "GSM331242", "GSM331243", "GSM331244", "GSM331245", "GSM331246", "GSM331247", "GSM331248", "GSM331249", "GSM331250", "GSM331251", "GSM331252", "GSM331253", "GSM331254", "GSM331255", "GSM331256", "GSM331257", "GSM331258", "GSM331259", "GSM331260", "GSM331261", "GSM331262", "GSM331263", "GSM331264", "GSM331265", "GSM331266", "GSM331267", "GSM331268", "GSM331269", "GSM331270", "GSM331271", "GSM331272", "GSM331273", "GSM331274", "GSM331275", "GSM331276", "GSM331277", "GSM331278", "GSM331279", "GSM331280", "GSM331281", "GSM331282", "GSM331283", "GSM331284", "GSM331285", "GSM331286", "GSM331287", "GSM331288", "GSM331289", "GSM331290", "GSM331291", "GSM331292", "GSM331293", "GSM331294", "GSM331295", "GSM331296", "GSM331297", "GSM331298", "GSM331299", "GSM331300", "GSM331301", "GSM331302", "GSM331303", "GSM331304", "GSM331305", "GSM331306", "GSM331307", "GSM331308", "GSM331309", "GSM331310", "GSM331311", "GSM331312", "GSM331313", "GSM331314", "GSM331315", "GSM331316", "GSM331317", "GSM331318", "GSM331319", "GSM331320", "GSM331321", "GSM331322", "GSM331323", "GSM331324", "GSM331325", "GSM331326", "GSM331327", "GSM331328", "GSM331329", "GSM331330", "GSM331331", "GSM331332", "GSM331333", "GSM331334", "GSM331335", "GSM331336", "GSM331337", "GSM331338", "GSM331339", "GSM331340", "GSM331341", "GSM331342", "GSM331343", "GSM331344", "GSM331345", "GSM331346", "GSM331347", "GSM331348", "GSM331349", "GSM331350", "GSM331351", "GSM331352", "GSM331353", "GSM331354", "GSM331355", "GSM331356", "GSM331357", "GSM331358", "GSM331359", "GSM331360", "GSM331361", "GSM331362", "GSM331363", "GSM331364", "GSM331365", "GSM331366", "GSM331367", "GSM331368", "GSM331369", "GSM331370", "GSM331371", "GSM331372", "GSM331373", "GSM331374", "GSM331375", "GSM331376", "GSM331377", "GSM331378", "GSM331379", "GSM331380", "GSM331381", "GSM331382", "GSM331383", "GSM331384", "GSM331385", "GSM331386", "GSM331387", "GSM331388", "GSM331389", "GSM331390", "GSM331391", "GSM331392", "GSM331393", "GSM331394", "GSM331395", "GSM331396", "GSM331397", "GSM331398", "GSM331399", "GSM331400", "GSM331401", "GSM331402", "GSM331403", "GSM331404", "GSM331405", "GSM331406", "GSM331407", "GSM331408", "GSM331409", "GSM331410", "GSM331411", "GSM331412", "GSM331413", "GSM331414", "GSM331415", "GSM331416", "GSM331417", "GSM331418", "GSM331419", "GSM331420", "GSM331421", "GSM331422", "GSM331423", "GSM331424", "GSM331425", "GSM331426", "GSM331427", "GSM331428", "GSM331429", "GSM331430", "GSM331431", "GSM331432", "GSM331433", "GSM331434", "GSM331435", "GSM331436", "GSM331437", "GSM331438", "GSM331439", "GSM331440", "GSM331441", "GSM331442", "GSM331443", "GSM331444", "GSM331445", "GSM331446", "GSM331447", "GSM331448", "GSM331449", "GSM331450", "GSM331451", "GSM331452", "GSM331453", "GSM331454", "GSM331455", "GSM331456", "GSM331457", "GSM331458", "GSM331459", "GSM331460", "GSM331461", "GSM331462", "GSM331463", "GSM331464", "GSM331465", "GSM331466", "GSM331467", "GSM331468", "GSM331469", "GSM331470", "GSM331471", "GSM331472", "GSM331473", "GSM331474", "GSM331475", "GSM331476", "GSM331477", "GSM331478", "GSM331479", "GSM331480", "GSM331481", "GSM331482", "GSM331483", "GSM331484", "GSM331485", "GSM331486", "GSM331487", "GSM331488", "GSM331489", "GSM331490", "GSM331491", "GSM331492", "GSM331493", "GSM331494", "GSM331495", "GSM331496", "GSM331497", "GSM331498", "GSM331499", "GSM331500", "GSM331501", "GSM331502", "GSM331503", "GSM331504", "GSM331505", "GSM331506", "GSM331507", "GSM331508", "GSM331509", "GSM331510", "GSM331511", "GSM331512", "GSM331513", "GSM331514", "GSM331515", "GSM331516", "GSM331517", "GSM331518", "GSM331519", "GSM331520", "GSM331521", "GSM331522", "GSM331523", "GSM331524", "GSM331525", "GSM331526", "GSM331527", "GSM331528", "GSM331529", "GSM331530", "GSM331531", "GSM331532", "GSM331533", "GSM331534", "GSM331535", "GSM331536", "GSM331537", "GSM331538", "GSM331539", "GSM331540", "GSM331541", "GSM331542", "GSM331543", "GSM331544", "GSM331545", "GSM331546", "GSM331547", "GSM331548", "GSM331549", "GSM331550", "GSM331551", 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:37476188", "data:geo:GSE13159"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13159"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:47:24Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 17714, "completion_tokens": 2815, "cached_tokens": 256}}, "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:37476188", "type": "paper", "label": "pmid:37476188"}, {"id": "source:pmid:37476188", "type": "manuscript", "label": "PMID 37476188 full text"}, {"id": "data:geo:GSE13159", "type": "dataset", "label": "GEO GSE13159"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37476188", "type": "paper", "label": "pmid:37476188"}, {"id": "source:pmid:37476188", "type": "manuscript", "label": "PMID 37476188 full text"}, {"id": "data:geo:GSE13159", "type": "dataset", "label": "GEO GSE13159"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37476188", "type": "extraction", "used": ["source:pmid:37476188"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13159", "type": "accession_resolution", "used": ["data:geo:GSE13159"], "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:37476188", "parent_hash": "sha256:59d1333502b2817644ac22a8cb072ca15a4264ce11327254fdac7ab2513bb447", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE13159 licence not read", "asset:data:geo:GSE13159 not downloaded", "asset:data:geo:GSE71014 licence not read", "asset:data:geo:GSE71014 not downloaded", "asset:data:geo:GSE9476 licence not read", "asset:data:geo:GSE9476 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "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": 0.69, "evidence": ["iferation in AML cell lines by enhancing the apoptosis and cell cycle arrest. 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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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Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. 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}}}