{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484252", "kind": "science-record", "revision": 8, "content_hash": "sha256:39480bbc60b4c36137b32ecc67bead004687e560e966f1aa176e122a06e631c5", "created_at": "2026-11-01T15:40:13Z", "updated_at": "2026-11-01T22:42:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiling of Gram-negative bacteria-induced inflammation in human whole blood: The role of complement and CD14-mediated innate immune response.", "doi": "10.1016/j.gdata.2015.05.019", "pmid": "26484252", "authors": ["Corinna Lau", "Ole Kristoffer Olstad", "Marit Holden", "Ståle Nygård", "Hilde Fure", "Knut Tore Lappegård", "Ole-Lars Brekke", "Terje Espevik", "Eivind Hovig", "Tom Eirik Mollnes"], "journal": "Genomics data", "year": 2015, "abstract": "Non-sterile pathogen-induced sepsis and sterile inflammation like in trauma or ischemia-reperfusion injury may both coincide with the life threatening systemic inflammatory response syndrome and multi-organ failure. Consequently, there is an urgent need for specific biomarkers in order to distinguish sepsis from sterile conditions. The overall aim of this study was to uncover putative sepsis biomarkers and biomarker pathways, as well as to test the efficacy of combined inhibition of innate immunity key players complement and Toll-like receptor co-receptor CD14 as a possible therapeutic regimen for sepsis. We performed whole blood gene expression analyses using microarray in order to profile Gram-negative bacteria-induced inflammatory responses in an ex vivo human whole blood model. The experiments were performed in the presence or absence of inhibitors of complement proteins (C3 and CD88 (C5a receptor 1)) and CD14, alone or in combination. In addition, we used blood from a C5-deficient donor. Anti-coagulated whole blood was challenged with heat-inactivated Escherichia coli for 2 h, total RNA was isolated and microarray analyses were performed on the Affymetrix GeneChip Gene 1.0 ST Array platform. The initial experiments were performed in duplicates using blood from two healthy donors. C5-deficiency is very rare, and only one donor could be recruited. In order to increase statistical power, a technical replicate of the C5-deficient samples was run. Subsequently, log2-transformed intensities were processed by robust multichip analysis and filtered using a threshold of four. In total, 73 microarray chips were run and analyzed. The normalized and filtered raw data have been deposited in NCBI's Gene Expression Omnibus (GEO) and are accessible with GEO Series accession number GSE55537. Linear models for microarray data were applied to estimate fold changes between data sets and the respective multiple testing adjusted p-values (FDR q-values). The interpretation of the data has been published by Lau et al. in an open access article entitled \"CD14 and Complement Crosstalk and Largely Mediate the Transcriptional Response to Escherichia coli in Human Whole Blood as revealed by DNA Microarray\" (Lau et al., 2015).", "claims": [{"id": "claim-method", "statement": "For interpretation of the results, which have been published elsewhere [1], the normalized and filtered log2 intensities of the 19,695 passed transcripts and for all 73 arrays were subjected to downstream statistical analyses using linear models for microarray data (Limma Bioconductor) [4], [5]. To correct for multiple testing, FDR q-values were computed from the p-values using the Benjamini–Hochberg method for controlling the false discovery rate (FDR) [6].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484252", "locator": "sections[8] \"Downstream statistical analyses\" paragraph 2", "quote": "For interpretation of the results, which have been published elsewhere [1], the normalized and filtered log2 intensities of the 19,695 passed transcripts and for all 73 arrays were subjected to downstream statistical analyses using linear models for microarray data (Limma Bioconductor) [4], [5]. To correct for multiple testing, FDR q-values were computed from the p-values using the Benjamini–Hochberg method for controlling the false discovery rate (FDR) [6]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The normalized and filtered log2-transformed intensities are available here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55537.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484252", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "The normalized and filtered log2-transformed intensities are available here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55537."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used linear models for microarray data to estimate fold changes and false-discovery-rate-adjusted p-values, and the source data are accessible through NCBI GEO accession GSE55537.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484252", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Linear models for microarray data were applied to estimate fold changes between data sets and the respective multiple testing adjusted p-values (FDR q-values)."}, {"asset": "source:pmid:26484252", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The normalized and filtered raw data have been deposited in NCBI's Gene Expression Omnibus (GEO) and are accessible with GEO Series accession number GSE55537."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used linear models for microarray data to estimate fold changes and false-discovery-rate-adjusted p-values, and the source data are accessible through NCBI GEO accession GSE55537.", "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:26484252"], "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:GSE55537"], "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": {"fdr_threshold": "with Benjamini–Hochberg false discovery rate correction"}, "inputs": ["data:geo:GSE55537"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484252", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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"GSM1338859", "GSM1338860", "GSM1338861", "GSM1338862", "GSM1338863", "GSM1338864", "GSM1338865", "GSM1338866", "GSM1338867", "GSM1338868", "GSM1338869", "GSM1338870", "GSM1338871", "GSM1338872", "GSM1338873", "GSM1338874", "GSM1338875", "GSM1338876", "GSM1338877", "GSM1338878", "GSM1338879", "GSM1338880", "GSM1338881", "GSM1338882", "GSM1338883", "GSM1338884", "GSM1338885", "GSM1338886", "GSM1338887", "GSM1338888"], "sample_count": 73, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "CD14 and complement crosstalk and largely mediate the transcriptional response to Escherichia coli in human whole blood as revealed by DNA microarray", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26484252:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bd342ab7ee40213a4f5fa5aae052e9c66a6a9e2931f8e919b58b30bac1e8efdf", "bytes": 10499, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#t0005", "version": null, "note": "List of microarray data sets generated by this study.", "structure": {"pmcid": "PMC4583639", "section_index": 6, "section_title": "DNA microarray analysis", "row_count": 74, "column_count": 5}, "table": {"label": "Table 1", "caption": "List of microarray data sets generated by this study.", "rows": [["GEO sample ID", "Sample title", "CEL file", "Protocol", "Scan date"], ["GSM1338877", "C5DR_anti-CD14 + Compstatin_D1", "10_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day1, replicate 1", "6/5/2010"], ["GSM1338878", "C5DR_anti-CD14 + Compstatin_D1_No2", "10_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338879", "C5DR_anti-CD14 + Compstatin_D2", "10_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338859", "C5D_C5aR antagonist_D1", "11_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338860", "C5D_C5aR antagonist_D1_No2", "11_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338861", "C5D_C5aR antagonist_D2", "11_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, C5aR-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338880", "C5DR_C5aR antagonist_D1", "12_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338881", "C5DR_C5aR antagonist_D1_No2", "12_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338882", "C5DR_C5aR antagonist_D2", "12_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, C5aR-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338862", "C5D_inhibitor ctrl_D1", "13_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338883", "C5DR_inhibitor ctrl_D1", "14_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338863", "C5D_inhibitor ctrl_D1_No2", "15_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338864", "C5D_inhibitor ctrl_D2", "15_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, inhibitor controls, 120 min, day 2", "5/13/2010"], ["GSM1338884", "C5DR_inhibitor ctrl_D1_No2", "16_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338885", "C5DR_inhibitor ctrl_D2", "16_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, inhibitor controls, 120 min, day 2", "5/13/2010"], ["GSM1338816", "ctrl2_PBS_D1", "17_C2_D1.CEL", "Healthy donor 2, PBS, 120 min, day 1", "5/20/2010"], ["GSM1338817", "ctrl2_PBS_D2", "17_C2_D2.CEL", "Healthy donor 2, PBS, 120 min, day 2", "5/28/2010"], ["GSM1338818", "ctrl_PBS_D1", "17_C5_D1.CEL", "Healthy donor 1, PBS, 120 min, day 1", "5/20/2010"], ["GSM1338819", "ctrl_PBS_D2", "17_C5_D2.CEL", "Healthy donor 1, PBS, 120 min, day 2", "5/28/2010"], ["GSM1338820", "ctrl2_E.coli_D1", "18_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, uninhibited, 120 min, day 1", "5/20/2010"], ["GSM1338821", "ctrl2_E.coli_D2", "18_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, uninhibited, 120 min, day 2", "5/28/2010"], ["GSM1338822", "ctrl_E.coli_D1", "18_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, uninhibited, 120 min, day 1", "5/20/2010"], ["GSM1338823", "ctrl_E.coli_D2", "18_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, uninhibited, 120 min, day 2", "5/28/2010"], ["GSM1338824", "ctrl2_Compstatin_D1", "19_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338825", "ctrl2_Compstatin_D2", "19_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, C3-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338826", "ctrl_Compstatin_D1", "19_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338827", "ctrl_Compstatin_D2", "19_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, C3-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338844", "C5D_PBS_D1", "1_C5_D1.CEL", "C5 deficient, PBS, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338845", "C5D_PBS_D1_No2", "1_C5_D1_Nr2.CEL", "C5 deficient, PBS, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338846", "C5D_PBS_D2", "1_C5_D2.CEL", "C5 deficient, PBS, 120 min, day 2", "5/13/2010"], ["GSM1338828", "ctrl2_anti-CD14_D1", "20_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338829", "ctrl2_anti-CD14_D2", "20_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, CD14-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338830", "ctrl_anti-CD14_D1", "20_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338831", "ctrl_anti-CD14_D2", "20_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, CD14-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338832", "ctrl2_anti-CD14 + Compstatin_D1", "21_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338833", "ctrl2_anti-CD14 + Compstatin_D2", "21_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338834", "ctrl_anti-CD14 + Compstatin_D1", "21_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338835", "ctrl_anti-CD14 + Compstatin_D2", "21_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338836", "ctrl2_C5aR antagonist_D1", "22_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338837", "ctrl2_C5aR antagonist_D2", "22_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, C5aR-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338838", "ctrl_C5aR antagonist_D1", "22_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338839", "ctrl_C5aR antagonist_D2", "22_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, C5aR-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338840", "ctrl2_inhibitor ctrl_D1", "24_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1", "5/20/2010"], ["GSM1338841", "ctrl2_inhibitor ctrl_D2", "24_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, inhibitor controls, 120 min, day 2", "5/28/2010"], ["GSM1338842", "ctrl_inhibitor ctrl_D1", "24_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1", "5/20/2010"], ["GSM1338843", "ctrl_inhibitor ctrl_D2", "24_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, inhibitor controls, 120 min, day 2", "5/28/2010"], ["GSM1338865", "C5DR_PBS_D1", "2_C5_D1.CEL", "C5 deficient, C5-reconstituted, PBS, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338866", "C5DR_PBS_D1_No2", "2_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, PBS, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338867", "C5DR_PBS_D2", "2_C5_D2.CEL", "C5 deficient, C5-reconstituted, PBS, 120 min, day 2", "5/13/2010"], ["GSM1338847", "C5D_E.coli_D1", "3_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, uninhibited, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338848", "C5D_E.coli_D1_No2", "3_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, uninhibited, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338849", "C5D_E.coli_D2", "3_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, uninhibited, 120 min, day 2", "5/13/2010"], ["GSM1338868", "C5DR_E.coli_D1", "4_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, uninhibited, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338869", "C5DR_E.coli_D1_No2", "4_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, uninhibited, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338870", "C5DR_E.coli_D2", "4_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, uninhibited, 120 min, day 2", "5/13/2010"], ["GSM1338850", "C5D_Compstatin_D1", "5_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338851", "C5D_Compstatin_D1_No2", "5_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338852", "C5D_Compstatin_D2", "5_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, C3-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338871", "C5DR_Compstatin_D1", "6_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1, replicate 1", "6/3/2010"], ["GSM1338872", "C5DR_Compstatin_D1_No2", "6_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338873", "C5DR_Compstatin_D2", "6_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, C3-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338853", "C5D_anti-CD14_D1", "7_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338854", "C5D_anti-CD14_D1_No2", "7_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338855", "C5D_anti-CD14_D2", "7_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, CD14-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338874", "C5DR_anti-CD14_D1", "8_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338875", "C5DR_anti-CD14_D1_No2", "8_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338876", "C5DR_anti-CD14_D2", "8_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, CD14-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338856", "C5D_anti-CD14 + Compstatin_D1", "9_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338857", "C5D_anti-CD14 + Compstatin_D1_No2", "9_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338858", "C5D_anti-CD14 + Compstatin_D2", "9_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338886", "ctrl2_T0_D2", "K2_T0_Dag2.CEL", "Healthy donor 2, PBS, 0 min, day 2", "5/28/2010"], ["GSM1338887", "ctrl_T0_D2", "K5_T0_Dag2.CEL", "Healthy donor 1, PBS, 0 min, day 2", "5/28/2010"], ["GSM1338888", "C5D_T0_D2", "T0_Dag1_C5_D2.CEL", "C5 deficient, PBS, 0 min, day 2", "5/13/2010"]], "row_count": 74, "column_count": 5, "numeric_cells": 309, "header_rows": 1, "locator": "section[6]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:GSE55537 not downloaded", "asset:data:geo:GSE55537 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fdr_threshold": "with Benjamini–Hochberg false discovery rate correction"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For interpretation of the results, which have been published elsewhere [1], the normalized and filtered log2 intensities of the 19,695 passed transcripts and for all 73 arrays were subjected to downstream statistical analyses using linear models for microarray data (Limma Bioconductor) [4], [5]. To correct for multiple testing, FDR q-values were computed from the p-values using the Benjamini–Hochberg method for controlling the false discovery rate (FDR) [6]."}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE55537"], "resolved_accessions": ["GSE55537"], "statements": ["The normalized and filtered log2-transformed intensities are available here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55537."], "basis": "The paper names GSE55537 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:26484252", "data:geo:GSE55537", "asset:table:pmid:26484252:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE55537"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:47Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 54867, "completion_tokens": 3107, "cached_tokens": 14658}}, "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:26484252", "type": "paper", "label": "pmid:26484252"}, {"id": "source:pmid:26484252", "type": "manuscript", "label": "PMID 26484252 full text"}, {"id": "data:geo:GSE55537", "type": "dataset", "label": "GEO GSE55537"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484252", "type": "paper", "label": "pmid:26484252"}, {"id": "source:pmid:26484252", "type": "manuscript", "label": "PMID 26484252 full text"}, {"id": "data:geo:GSE55537", "type": "dataset", "label": "GEO GSE55537"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484252", "type": "extraction", "used": ["source:pmid:26484252"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE55537", "type": "accession_resolution", "used": ["data:geo:GSE55537"], "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:26484252", "parent_hash": "sha256:fd46517acf50e1460f56a4720d19cc120176389e18e6149337daa11c5e8ff397", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE55537 licence not read", "asset:data:geo:GSE55537 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d whole blood gene expression analyses using microarray in order to profile Gram-negative bacteria-i", "hia coli for 2 h, total RNA was isolated and microarray analyses were performed on the Affymetrix Ge", "ered using a threshold of four. In total, 73 microarray chips were run and analyzed. The normalized", "accession number GSE55537. Linear models for microarray data were applied to estimate fold changes b"], "order_basis": "paper_text_order:784", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["For interpretation of the results, which have been published elsewhere [1], the normalized and filtered log2 intensities of the 19,695 passed transcripts and for all 73 arrays were subjected to downstream statistical analyses using linear models for microarray data (Limma Bioconductor) [4], [5]. To correct for multiple testing, FDR q-values were computed from the p-values using the Benjamini–Hochberg method for controlling the false discovery rate (FDR) [6]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T03:59:30+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}}}