Identification of Biomarkers for Sepsis-Induced Acute Lung Injury Through Bioinformatics and Machine Learning Approaches, with Experimental Validation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41070114", "kind": "science-record", "revision": 4, "content_hash": "sha256:158bfc214b4e5a59de9de8403fa9fb7d21d051e7207b56402b811f031ed00717", "created_at": "2026-11-01T20:31:07Z", "updated_at": "2026-11-01T22:57:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Biomarkers for Sepsis-Induced Acute Lung Injury Through Bioinformatics and Machine Learning Approaches, with Experimental Validation.", "doi": "10.2147/JIR.S539899", "pmid": "41070114", "authors": ["Yannian Luo", "Juan Xu", "Nannan He", "Wen Cao"], "journal": "Journal of inflammation research", "year": 2025, "abstract": "Background: Sepsis-induced acute lung injury (ALI) remains a life-threatening condition due to the lack of reliable early diagnostic biomarkers. Machine learning offers powerful tools for analyzing high-dimensional gene expression data and identifying potential biomarkers and therapeutic targets.\nMethods: Five datasets (GSE10474, GSE32707, GSE66890, GSE10361, GSE3037) were obtained from the GEO database. After assessment and normalization, GSE10474, GSE32707, and GSE66890 were combined as a training set to identify differentially expressed genes (DEGs). DEGs were intersected with genes from key modules identified by weighted gene co-expression network analysis (WGCNA), yielding 213 overlapping genes. These were analyzed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Eight machine learning algorithms (RF, SVM, GLM, GBM, KNN, NNET, LASSO, DT) were used to develop diagnostic models, which were validated on GSE10361 and GSE3037. Model performance was evaluated using a nomogram, calibration curves, and decision curve analysis (DCA). Immune and inflammatory states were assessed using the CIBERSORT algorithm. Potential therapeutic compounds were identified through the DSigDB database via the Enrichr platform. Molecular docking and molecular dynamics simulations examined interactions between Resveratrol and selected targets. In vitro experiments validated these findings.\nResults: A total of 213 candidate genes were identified by intersecting DEGs with WGCNA-derived MEblue module genes. GO and KEGG analyses indicated associations with immune activation and bacterial infection. Four key genes (DDAH2, PNPLA2, STXBP2, TCN1) were selected using eight machine learning algorithms. The diagnostic model showed good performance via nomogram, calibration curve, and DCA. Molecular docking revealed stable binding of Resveratrol to these genes. In vitro, Resveratrol pretreatment alleviated LPS-induced ALI by modulating the core genes.\nConclusion: The four genes may serve as diagnostic biomarkers for sepsis-ALI. Resveratrol represents a potential therapeutic strategy by targeting these genes.", "claims": [{"id": "claim-method", "statement": "Data were analyzed using one-way ANOVA with GraphPad Prism 9.0, considering p-values less than 0.05 as statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41070114", "locator": "sections[14] \"Statistical Analysis\" paragraph 2", "quote": "Data were analyzed using one-way ANOVA with GraphPad Prism 9.0, considering p-values less than 0.05 as statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41070114", "locator": "sections[28] \"Data Sharing Statement\" paragraph 2", "quote": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field."}], "state": "complete"}, {"id": "claim-target-result", "statement": "ROC curve analysis further supported the discriminative power of the model.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41070114", "locator": "sections[20] \"Establishment of Diagnostic Prediction Model\" paragraph 2", "quote": "The nomogram achieved an AUC of 0.834, while the individual genes also exhibited good diagnostic performance: DDAH2 (AUC = 0.792), PNPLA2 (AUC = 0.709), STXBP2 (AUC = 0.721), and TCN1 (AUC = 0.770) (Figure 5D)."}, {"asset": "source:pmid:41070114", "locator": "sections[20] \"Establishment of Diagnostic Prediction Model\" paragraph 2", "quote": "ROC curve analysis further supported the discriminative power of the model."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ROC curve analysis further supported the discriminative power of the model.", "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:41070114"], "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:GSE10361"], "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:GSE10361"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41070114", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/JIR.S539899", "sha256": "sha256:b43450087b9693e467b434648c0e1e98f70a3d4031ad8ac2b05659ebfe6facab", "bytes": 41060, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/JIR.S539899", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12506793", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10361", "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=GSE10361", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10361", "version": null, "note": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM260537", "GSM260541", "GSM260542", "GSM261573", "GSM261575", "GSM261580", "GSM261581", "GSM261913", "GSM261914"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Temporal Analysis of Platelets as Cytotoxic Mediators in Sepsis-induced Acute Lung Injury (ALI)", "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:GSE10474", "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=GSE10474", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10474", "version": null, "note": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM264753", "GSM264987", "GSM264988", "GSM264989", "GSM264990", "GSM264991", "GSM264992", "GSM264994", "GSM264995", "GSM264996", "GSM264998", "GSM265000", "GSM265001", "GSM265004", "GSM265006", "GSM265008", "GSM265009", "GSM265011", "GSM265014", "GSM265016", "GSM265018", "GSM265019", "GSM265021", "GSM265022", "GSM265023", "GSM265024", "GSM265026", "GSM265027", "GSM265028", "GSM265029", "GSM265030", "GSM265031", "GSM265032", "GSM265033"], "sample_count": 34, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Microarray Analysis of Acute Lung Injury", "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:GSE3037", "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=GSE3037", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE3037", "version": null, "note": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM66867", "GSM66868", "GSM66869", "GSM66870", "GSM66871", "GSM66872", "GSM66873", "GSM66874", "GSM66875", "GSM66876", "GSM66877", "GSM66878", "GSM66879", "GSM66880", "GSM66881", "GSM66882", "GSM66883", "GSM66884", "GSM66885", "GSM66886", "GSM66887", "GSM66888", "GSM66889", "GSM66890"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Stimulation by LPS and HMGB1 in peripheral blood neutrophils from patients with sepsis-induced acute lung injury", "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:GSE32707", "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=GSE32707", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32707", "version": null, "note": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM812609", "GSM812610", "GSM812611", "GSM812612", "GSM812613", "GSM812614", "GSM812615", "GSM812616", "GSM812617", "GSM812618", "GSM812619", "GSM812620", "GSM812621", "GSM812622", "GSM812623", "GSM812624", "GSM812625", "GSM812626", "GSM812627", "GSM812628", "GSM812629", "GSM812630", "GSM812631", "GSM812632", "GSM812633", "GSM812634", "GSM812635", "GSM812636", "GSM812637", "GSM812638", "GSM812639", "GSM812640", "GSM812641", "GSM812642", "GSM812643", "GSM812644", "GSM812645", "GSM812646", "GSM812647", "GSM812648", "GSM812649", "GSM812650", "GSM812651", "GSM812652", "GSM812653", "GSM812654", "GSM812655", "GSM812656", "GSM812657", "GSM812658", "GSM812659", "GSM812660", "GSM812661", "GSM812662", "GSM812663", "GSM812664", "GSM812665", "GSM812666", "GSM812667", "GSM812668", "GSM812669", "GSM812670", "GSM812671", "GSM812672", "GSM812673", "GSM812674", "GSM812675", "GSM812676", "GSM812677", "GSM812678", "GSM812679", "GSM812680", "GSM812681", "GSM812682", "GSM812683", "GSM812684", "GSM812685", "GSM812686", "GSM812687", "GSM812688", "GSM812689", "GSM812690", "GSM812691", "GSM812692", "GSM812693", "GSM812694", "GSM812695", "GSM812696", "GSM812697", "GSM812698", "GSM812699", "GSM812700", "GSM812701", "GSM812702", "GSM812703", "GSM812704", "GSM812705", "GSM812706", "GSM812707", "GSM812708", "GSM812709", "GSM812710", "GSM812711", "GSM812712", "GSM812713", "GSM812714", "GSM812715", "GSM812716", "GSM812717", "GSM812718", "GSM812719", "GSM812720", "GSM812721", "GSM812722", "GSM812723", "GSM812724", "GSM812725", "GSM812726", "GSM812727", "GSM812728", "GSM812729", "GSM812730", "GSM812731", "GSM812732", "GSM812733", "GSM812734", "GSM812735", "GSM812736", "GSM812737", "GSM812738", "GSM812739", "GSM812740", "GSM812741", "GSM812742", "GSM812743", "GSM812744", "GSM812745", "GSM812746", "GSM812747", "GSM812748", "GSM812749", "GSM812750", "GSM812751", "GSM812752"], "sample_count": 144, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Inflammasome-regulated cytokines are critical mediators of lung injury in humans.", "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:GSE66890", "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=GSE66890", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66890", "version": null, "note": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1633778", "GSM1633779", "GSM1633780", "GSM1633781", "GSM1633782", "GSM1633783", "GSM1633784", "GSM1633785", "GSM1633786", "GSM1633787", "GSM1633788", "GSM1633789", "GSM1633790", "GSM1633791", "GSM1633792", "GSM1633793", "GSM1633794", "GSM1633795", "GSM1633796", "GSM1633797", "GSM1633798", "GSM1633799", "GSM1633800", "GSM1633801", "GSM1633802", "GSM1633803", "GSM1633804", "GSM1633805", "GSM1633806", "GSM1633807", "GSM1633808", "GSM1633809", "GSM1633810", "GSM1633811", "GSM1633812", "GSM1633813", "GSM1633814", "GSM1633815", "GSM1633816", "GSM1633817", "GSM1633818", "GSM1633819", "GSM1633820", "GSM1633821", "GSM1633822", "GSM1633823", "GSM1633824", "GSM1633825", "GSM1633826", "GSM1633827", "GSM1633828", "GSM1633829", "GSM1633830", "GSM1633831", "GSM1633832", "GSM1633833", "GSM1633834", "GSM1633835", "GSM1633836", "GSM1633837", "GSM1633838", "GSM1633839"], "sample_count": 62, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Expression of Neutrophil-related genes in patients with early sepsis-induced ARDS", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE10361 not downloaded", "asset:data:geo:GSE10361 licence not read", "asset:data:geo:GSE10474 not downloaded", "asset:data:geo:GSE10474 licence not read", "asset:data:geo:GSE3037 not downloaded", "asset:data:geo:GSE3037 licence not read", "asset:data:geo:GSE32707 not downloaded", "asset:data:geo:GSE32707 licence not read", "asset:data:geo:GSE66890 not downloaded", "asset:data:geo:GSE66890 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Data were analyzed using one-way ANOVA with GraphPad Prism 9.0, considering p-values less than 0.05 as statistically significant."}}, {"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": 0.7, "band": "medium", "quote": "SVM"}}, {"id": "method-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC Curve"}}, {"id": "method-4", "family": "model_calibration", "specific": "decision_curve", "label": "Model calibration / clinical utility", "dsl_operations": ["calibration_bins", "net_benefit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictions_and_outcomes"], "evidence": {"score": 0.7, "band": "medium", "quote": "decision curve analysis"}}], "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["GSE10474", "GSE32707", "GSE66890", "GSE10361", "GSE3037"], "resolved_accessions": ["GSE10474", "GSE32707", "GSE66890", "GSE10361", "GSE3037"], "statements": ["The data underlying this study’s conclusions can be obtained from the corresponding author upon reasonable request. This aligns with the principles of open science, enabling independent verification and facilitating future research by others in the field."], "basis": "The paper names GSE10474, GSE32707, GSE66890, GSE10361, GSE3037 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:41070114", "data:geo:GSE10361"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10361"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:02:48Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10858, "completion_tokens": 1651, "cached_tokens": 0}}, "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:41070114", "type": "paper", "label": "pmid:41070114"}, {"id": "source:pmid:41070114", "type": "manuscript", "label": "PMID 41070114 full text"}, {"id": "data:geo:GSE10361", "type": "dataset", "label": "GEO GSE10361"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41070114", "type": "paper", "label": "pmid:41070114"}, {"id": "source:pmid:41070114", "type": "manuscript", "label": "PMID 41070114 full text"}, {"id": "data:geo:GSE10361", "type": "dataset", "label": "GEO GSE10361"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41070114", "type": "extraction", "used": ["source:pmid:41070114"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10361", "type": "accession_resolution", "used": ["data:geo:GSE10361"], "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:41070114", "parent_hash": "sha256:089057dec5ba9e4151a674bf1b1c5c430a9a691e3b37413d687cd75d0fd9eaa0", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE10361 licence not read", "asset:data:geo:GSE10361 not downloaded", "asset:data:geo:GSE10474 licence not read", "asset:data:geo:GSE10474 not downloaded", "asset:data:geo:GSE3037 licence not read", "asset:data:geo:GSE3037 not downloaded", "asset:data:geo:GSE32707 licence not read", "asset:data:geo:GSE32707 not downloaded", "asset:data:geo:GSE66890 licence not read", "asset:data:geo:GSE66890 not downloaded", "execution.not_run", "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": 0.99, "evidence": ["ts with sepsis-related ALI. Cell Culture and Viability Assay The human bronchial epithelial cell line BEA", "ing treatment, 10 µL of Cell Counting Kit-8 (CCK-8; Solarbio, China) reagent was added to each"], "order_basis": "paper_text_order:3325", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Data were analyzed using one-way ANOVA with GraphPad Prism 9.0, considering p-values less than 0.05 as statistically significant."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}