{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39251710", "kind": "science-record", "revision": 3, "content_hash": "sha256:2dd2a7dc193f2a200f1ac37e63ada2ca231e69f3f18e54c07db4fe13b027e472", "created_at": "2026-11-01T20:29:23Z", "updated_at": "2026-11-01T22:12:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development of a prognostic model for NSCLC based on differential genes in tumour stem cells.", "doi": "10.1038/s41598-024-71317-2", "pmid": "39251710", "authors": ["Yuqi Ma", "Jiawei Li", "Chunping Xiong", "Xiaoluo Sun", "Tao Shen"], "journal": "Scientific reports", "year": 2024, "abstract": "Non-small cell lung cancer (NSCLC) constitutes a significant portion of lung cancers and cytotoxic drugs (e.g. cisplatin) are currently the first-line treatment. However, NSCLC has developed resistance to this drug, which limits the therapeutic effect and thus affects prognosis. NSCLC sc-RNA-seq data were downloaded from the GEO database and Ku Leuven Laboratory for Functional Epigenetics, and bulk RNA-seq data were obtained from the TCGA database. The \"Seurat\" package was employed for scRNA-seq data processing, and the uniform manifold approximation and projection (UMAP) were applied for downscaling and cluster identification. Use the FindAllMarkers function to find differential genes (DEGs) for tumor stem cells. Then, we performed univariate regression analyses on the DEGs to identify potential prognostic genes. We created a machine learning framework based on potential prognostic genes, which combines 10 machine learning methods and their 101 combinations to get the optimal prognostic risk model. The model was evaluated in the training set and validation set. A nomogram was developed to provide physicians with a quantitative tool for prognosis prediction. Finally, we evaluated the expression and functionality of SLC2A1. We discovered 22 cell clusters containing 218379 cells by examining single-cell RNA sequencing datasets (GSE148071, KU_lom, GSE131907, GSE136246, GSE127465). Tumour cells were isolated for subpopulation analysis and 162 differential genes from SOX2_cancer were obtained. After univariate Cox analysis, we found 23 genes with prognostic potential prognostic value and utilized them to develop 101‑combination machine learning computational framework. We eventually picked the best performing 'StepCox[both] + RSF', which includes 8 genes. The model has a relatively high prediction accuracy in both TCGA and GEO datasets. In in vitro investigations, targeted suppression of the SLC2A1 gene resulted in significant reductions in proliferation, invasion and migration in A549 cells. In addition, a significant reduction in cisplatin resistance was seen in A549/DDP cells. The outcomes demonstrated the precision and credibility of the prognostic model for NSCLC, highlighting its potential significance in the treatment and prognosis of individuals affected by this disease. SLC2A1 may become a promising prognostic marker and a potential therapeutic target, offering valuable insights to inform clinical treatment decisions.", "claims": [{"id": "claim-method", "statement": "We used ten machine learning methods—ridge regression, least absolute shrinkage and selection operator (Lasso) regression, stepwise Cox regression, CoxBoost, random survival forest (RSF), elastic network (Enet), plsRcox, supervised principal component (SuperPC), survival support vector machine (SVM) and gradient boosting machine (GBM) (The details of each method can be found in Attachment 4a). These methods were combined into 101 unique combinations for variable selection and model formulation. Finally, we evaluated the effectiveness of our models on the training and validation datasets using a consistency index (C-index) and then calculated the average scores.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39251710", "locator": "sections[5] \"Prognostic model construction and validation\" paragraph 2", "quote": "We used ten machine learning methods—ridge regression, least absolute shrinkage and selection operator (Lasso) regression, stepwise Cox regression, CoxBoost, random survival forest (RSF), elastic network (Enet), plsRcox, supervised principal component (SuperPC), survival support vector machine (SVM) and gradient boosting machine (GBM) (The details of each method can be found in Attachment 4a). These methods were combined into 101 unique combinations for variable selection and model formulation. Finally, we evaluated the effectiveness of our models on the training and validation datasets using a consistency index (C-index) and then calculated the average scores."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39251710", "locator": "sections[34] \"notes\" paragraph 1", "quote": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The optimal NSCLC prognostic model was StepCox[both] + RSF, which achieved the highest average C-index of 0.796.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39251710", "locator": "sections[17] \"Validation of the prognostic model\" paragraph 2", "quote": "The results showed that the combination of ‘StepCox[both] + RSF’ had the highest average C-index (0.796) (Fig. 3a)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The optimal NSCLC prognostic model was StepCox[both] + RSF, which achieved the highest average C-index of 0.796.", "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:39251710"], "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:GSE127465"], "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:GSE127465"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39251710", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-71317-2", "sha256": "sha256:72ffcf1dc7d98f3e030639459ace177b7395ebbe101be3dfcdbeb9d00d4752d4", "bytes": 30349, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-71317-2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11383933", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE127465", "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=GSE127465", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE127465", "version": null, "note": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3635278", "GSM3635279", "GSM3635280", "GSM3635281", "GSM3635282", "GSM3635283", "GSM3635284", "GSM3635285", "GSM3635286", "GSM3635287", "GSM3635288", "GSM3635289", "GSM3635290", "GSM3635291", "GSM3635292", "GSM3635293", "GSM3635294", "GSM3635295", "GSM3635296", "GSM3635297", "GSM3635298", "GSM3635299", "GSM3635300", "GSM3635301", "GSM3635302", "GSM3635303", "GSM3635304", "GSM3635305", "GSM3635306", "GSM3635307", "GSM3635308", "GSM3635309", "GSM3635310", "GSM3635311", "GSM3635312", "GSM3635313", "GSM3635314", "GSM3635315", "GSM3635316", "GSM3635317"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "19057;18573", "taxon": "Mus musculus; Homo sapiens", "title": "Single cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE131907", "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=GSE131907", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE131907", "version": null, "note": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3827114", "GSM3827115", "GSM3827116", "GSM3827117", "GSM3827118", "GSM3827119", "GSM3827120", "GSM3827121", "GSM3827122", "GSM3827123", "GSM3827124", "GSM3827125", "GSM3827126", "GSM3827127", "GSM3827128", "GSM3827129", "GSM3827130", "GSM3827131", "GSM3827132", "GSM3827133", "GSM3827134", "GSM3827135", "GSM3827136", "GSM3827137", "GSM3827138", "GSM3827139", "GSM3827140", "GSM3827141", "GSM3827142", "GSM3827143", "GSM3827144", "GSM3827145", "GSM3827146", "GSM3827147", "GSM3827148", "GSM3827149", "GSM3827150", "GSM3827151", "GSM3827152", "GSM3827153", "GSM3827154", "GSM3827155", "GSM3827156", "GSM3827157", "GSM3827158", "GSM3827159", "GSM3827160", "GSM3827161", "GSM3827162", "GSM3827163", "GSM3827164", "GSM3827165", "GSM3827166", "GSM3827167", "GSM3827168", "GSM3827169", "GSM3827170", "GSM3827171"], "sample_count": 58, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "Single cell RNA sequencing of lung adenocarcinoma", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE13213", "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=GSE13213", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13213", "version": null, "note": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM333673", "GSM333674", "GSM333675", "GSM333676", "GSM333677", "GSM333678", "GSM333679", "GSM333680", "GSM333681", "GSM333682", "GSM333683", "GSM333684", "GSM333685", "GSM333686", "GSM333687", "GSM333688", "GSM333689", "GSM333690", "GSM333691", "GSM333692", "GSM333693", "GSM333694", "GSM333695", "GSM333696", "GSM333697", "GSM333698", "GSM333699", "GSM333700", "GSM333701", "GSM333702", "GSM333703", "GSM333704", "GSM333705", "GSM333706", "GSM333707", "GSM333708", "GSM333709", "GSM333710", "GSM333711", "GSM333712", "GSM333713", "GSM333714", "GSM333715", "GSM333716", "GSM333717", "GSM333718", "GSM333719", "GSM333720", "GSM333721", "GSM333722", "GSM333723", "GSM333724", "GSM333725", "GSM333726", "GSM333727", "GSM333728", "GSM333729", "GSM333730", "GSM333731", "GSM333732", "GSM333733", "GSM333734", "GSM333735", "GSM333736", "GSM333737", "GSM333738", "GSM333739", "GSM333740", "GSM333741", "GSM333742", "GSM333743", "GSM333744", "GSM333745", "GSM333746", "GSM333747", "GSM333748", "GSM333749", "GSM333750", "GSM333751", "GSM333752", "GSM333753", "GSM333754", "GSM333755", "GSM333756", "GSM333757", "GSM333758", "GSM333759", "GSM333760", "GSM333761", "GSM333762", "GSM333763", "GSM333764", "GSM333765", "GSM333766", "GSM333767", "GSM333768", "GSM333769", "GSM333770", "GSM333771", "GSM333772", "GSM333773", "GSM333774", "GSM333775", "GSM333776", "GSM333777", "GSM333778", "GSM333779", "GSM333780", "GSM333781", "GSM333782", "GSM333783", "GSM333784", "GSM333785", "GSM333786", "GSM333787", "GSM333788", "GSM333789"], "sample_count": 117, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Relapse-related molecular signature in lung adenocarcinomas identifies patients with dismal prognosis", "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:GSE136246", "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=GSE136246", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE136246", "version": null, "note": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4043230", "GSM4043231", "GSM4043232", "GSM4043233", "GSM4043234", "GSM4043235", "GSM4043236", "GSM4043237", "GSM4043238", "GSM4043239", "GSM4043240", "GSM4043241", "GSM4043242", "GSM4043243", "GSM4043244", "GSM4043245", "GSM4043246", "GSM4043247", "GSM4043248", "GSM4043249", "GSM4043250", "GSM4043251", "GSM4043252", "GSM4043253", "GSM4043254", "GSM4043255", "GSM4043256", "GSM4043257", "GSM4043258", "GSM4043259", "GSM4043260"], "sample_count": 31, "group_sizes": null, "group_sizes_basis": null, "platform": "24268;18573;27138", "taxon": "Homo sapiens; Mus musculus", "title": "Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE148071", "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=GSE148071", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE148071", "version": null, "note": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4453576", "GSM4453577", "GSM4453578", "GSM4453579", "GSM4453580", "GSM4453581", "GSM4453582", "GSM4453583", "GSM4453584", "GSM4453585", "GSM4453586", "GSM4453587", "GSM4453588", "GSM4453589", "GSM4453590", "GSM4453591", "GSM4453592", "GSM4453593", "GSM4453594", "GSM4453595", "GSM4453596", "GSM4453597", "GSM4453598", "GSM4453599", "GSM4453600", "GSM4453601", "GSM4453602", "GSM4453603", "GSM4453604", "GSM4453605", "GSM4453606", "GSM4453607", "GSM4453608", "GSM4453609", "GSM4453610", "GSM4453611", "GSM4453612", "GSM4453613", "GSM4453614", "GSM4453615", "GSM4453616", "GSM4453617"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "20795", "taxon": "Homo sapiens", "title": "Comprehensive Profiling of Cancer Cells and Their Microenvironment in Advanced NSCLC", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE29016", "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=GSE29016", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29016", "version": null, "note": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM718902", "GSM718903", "GSM718904", "GSM718905", "GSM718906", "GSM718907", "GSM718908", "GSM718909", "GSM718910", "GSM718911", "GSM718912", "GSM718913", "GSM718914", "GSM718915", "GSM718916", "GSM718917", "GSM718918", "GSM718919", "GSM718920", "GSM718921", "GSM718922", "GSM718923", "GSM718924", "GSM718925", "GSM718926", "GSM718927", "GSM718928", "GSM718929", "GSM718930", "GSM718931", "GSM718932", "GSM718933", "GSM718934", "GSM718935", "GSM718936", "GSM718937", "GSM718938", "GSM718939", "GSM718940", "GSM718941", "GSM718942", "GSM718943", "GSM718944", "GSM718945", "GSM718946", "GSM718947", "GSM718948", "GSM718949", "GSM718950", "GSM718951", "GSM718952", "GSM718953", "GSM718954", "GSM718955", "GSM718956", "GSM718957", "GSM718958", "GSM718959", "GSM718960", "GSM718961", "GSM718962", "GSM718963", "GSM718964", "GSM718965", "GSM718966", "GSM718967", "GSM718968", "GSM718969", "GSM718970", "GSM718971", "GSM718972", "GSM718973"], "sample_count": 72, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Relation between smoking history and gene expression profiles in lung adenocarcinomas", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE127465 not downloaded", "asset:data:geo:GSE127465 licence not read", "asset:data:geo:GSE131907 not downloaded", "asset:data:geo:GSE131907 licence not read", "asset:data:geo:GSE13213 not downloaded", "asset:data:geo:GSE13213 licence not read", "asset:data:geo:GSE136246 not downloaded", "asset:data:geo:GSE136246 licence not read", "asset:data:geo:GSE148071 not downloaded", "asset:data:geo:GSE148071 licence not read", "asset:data:geo:GSE29016 not downloaded", "asset:data:geo:GSE29016 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used ten machine learning methods—ridge regression, least absolute shrinkage and selection operator (Lasso) regression, stepwise Cox regression, CoxBoost, random survival forest (RSF), elastic network (Enet), plsRcox, supervised principal component (SuperPC), survival support vector machine (SVM) and gradient boosting machine (GBM) (The details of each method can be found in Attachment 4a). These methods were combined into 101 unique combinations for variable selection and model formulation. Finally, we evaluated the effectiveness of our models on the training and validation datasets using a consistency index (C-index) and then calculated the average scores."}}, {"id": "method-2", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "support vector machine"}}, {"id": "method-3", "family": "machine_learning", "specific": "gradient_boosting", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "gradient boosting"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE148071", "GSE131907", "GSE136246", "GSE127465", "GSE29016", "GSE13213"], "resolved_accessions": ["GSE148071", "GSE131907", "GSE136246", "GSE127465", "GSE29016", "GSE13213"], "statements": ["We thank the TCGA and GEO databases for providing data. Single-cell data can be obtained by searching the official website according to the data number(s).TCGA: https://portal.gdc.cancer.gov/, GEO: https://www.ncbi.nlm.nih.gov/geo/. The dataset named KU_loom is available at (https://gbiomed.kuleuven.be/scRNAseq-NSCLC). The raw data of the in vitro experiments and the code of the R software can be obtained by contacting the corresponding author."], "basis": "The paper names GSE148071, GSE131907, GSE136246, GSE127465, GSE29016, GSE13213 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:39251710", "data:geo:GSE127465"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE127465"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:30:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8771, "completion_tokens": 2338, "cached_tokens": 264}}, "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:39251710", "type": "paper", "label": "pmid:39251710"}, {"id": "source:pmid:39251710", "type": "manuscript", "label": "PMID 39251710 full text"}, {"id": "data:geo:GSE127465", "type": "dataset", "label": "GEO GSE127465"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39251710", "type": "paper", "label": "pmid:39251710"}, {"id": "source:pmid:39251710", "type": "manuscript", "label": "PMID 39251710 full text"}, {"id": "data:geo:GSE127465", "type": "dataset", "label": "GEO GSE127465"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39251710", "type": "extraction", "used": ["source:pmid:39251710"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE127465", "type": "accession_resolution", "used": ["data:geo:GSE127465"], "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:39251710", "parent_hash": "sha256:4bf03817e9e2eb907506bc2825771631f440ba26b7d955bc52c6c1c26e6a10b6", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE127465 licence not read", "asset:data:geo:GSE127465 not downloaded", "asset:data:geo:GSE131907 licence not read", "asset:data:geo:GSE131907 not downloaded", "asset:data:geo:GSE13213 licence not read", "asset:data:geo:GSE13213 not downloaded", "asset:data:geo:GSE136246 licence not read", "asset:data:geo:GSE136246 not downloaded", "asset:data:geo:GSE148071 licence not read", "asset:data:geo:GSE148071 not downloaded", "asset:data:geo:GSE29016 licence not read", "asset:data:geo:GSE29016 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["effect and thus affects prognosis. NSCLC sc-RNA-seq data were downloaded from the GEO database a", "oratory for Functional Epigenetics, and bulk RNA-seq data were obtained from the TCGA database. T", "aining 218379 cells by examining single-cell RNA sequencing datasets (GSE148071, KU_lom, GSE131907, GSE1"], "order_basis": "paper_text_order:339", "id": "assay:1"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lusters containing 218379 cells by examining single-cell RNA sequencing datasets (GSE148071, KU_lom, GSE131907, GSE1", "abase. The \"Seurat\" package was employed for scRNA-seq data processing, and the uniform manifold ap"], "order_basis": "paper_text_order:540", "id": "assay:2"}, {"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": ["in proliferation, invasion and migration in A549 cells. In addition, a significant reduction", "eduction in cisplatin resistance was seen in A549/DDP cells. The outcomes demonstrated the pre"], "order_basis": "paper_text_order:2061", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We used ten machine learning methods—ridge regression, least absolute shrinkage and selection operator (Lasso) regression, stepwise Cox regression, CoxBoost, random survival forest (RSF), elastic network (Enet), plsRcox, supervised principal component (SuperPC), survival support vector machine (SVM) and gradient boosting machine (GBM) (The details of each method can be found in Attachment 4a). These methods were combined into 101 unique combinations for variable selection and model formulation. Finally, we evaluated the effectiveness of our models on the training and validation datasets using a consistency index (C-index) and then calculated the average scores."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. 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. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T00:47:34+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. 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. 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}}}