{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:23183685", "kind": "science-record", "revision": 5, "content_hash": "sha256:3fb7f6bb3cabe6d0624c3897cca1298b72818aa4d6a7991c1a8a1dad55d6ce94", "created_at": "2026-11-01T15:40:02Z", "updated_at": "2026-11-01T18:46:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A visual description of the dissection of the cerebral surface vasculature and associated meninges and the choroid plexus from rat brain.", "doi": "10.3791/4285", "pmid": "23183685", "authors": ["John F Bowyer", "Monzy Thomas", "Tucker A Patterson", "Nysia I George", "Jeffrey A Runnells", "Mark S Levi"], "journal": "Journal of visualized experiments : JoVE", "year": 2012, "abstract": "This video presentation was created to show a method of harvesting the two most important highly vascular structures, not residing within the brain proper, that support forebrain function. They are the cerebral surface (superficial) vasculature along with associated meninges (MAV) and the choroid plexus which are necessary for cerebral blood flow and cerebrospinal fluid (CSF) homeostasis. The tissue harvested is suitable for biochemical and physiological analysis, and the MAV has been shown to be sensitive to damage produced by amphetamine and hyperthermia. As well, the major and minor cerebral vasculatures harvested in MAV are of potentially high interest when investigating concussive types of head trauma. The MAV dissected in this presentation consists of the pial and some of the arachnoid membrane (less dura) of the meninges and the major and minor cerebral surface vasculature. The choroid plexus dissected is the structure that resides in the lateral ventricles as described by Oldfield and McKinley. The methods used for harvesting these two tissues also facilitate the harvesting of regional cortical tissue devoid of meninges and larger cerebral surface vasculature, and is compatible with harvesting other brain tissues such as striatum, hypothalamus, hippocampus, etc. The dissection of the two tissues takes from 5 to 10 min total. The gene expression levels for the dissected MAV and choroid plexus, as shown and described in this presentation can be found at GSE23093 (MAV) and GSE29733 (choroid plexus) at the NCBI GEO repository. This data has been, and is being, used to help further understand the functioning of the MAV and choroid plexus and how neurotoxic events such as severe hyperthermia and AMPH adversely affect their function.", "claims": [{"id": "claim-data-access", "statement": "The gene expression levels for the dissected MAV and choroid plexus, as shown and described in this presentation can be found at GSE23093 (MAV) and GSE29733 (choroid plexus) at the NCBI GEO repository.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23183685", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The gene expression levels for the dissected MAV and choroid plexus, as shown and described in this presentation can be found at GSE23093 (MAV) and GSE29733 (choroid plexus) at the NCBI GEO repository."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using Agilent whole-rat genome oligonucleotide arrays and volcano plots, the study found that MAV gene expression was markedly distinct from striatum and parietal cortex, with the source expression data available through NCBI GEO under GSE23093 and GSE29733.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:23183685", "locator": "sections[6] \"5. Representative Results\" paragraph 3", "quote": "The gene expression of more than 11,000 genes with official NCBI gene symbols in MAV of control animals was compared to those recorded in the striatum and parietal cortex. Over 2000 of these genes had a 2.5-fold or more differing expression in the MAV compared to the two neuronal-rich tissues, and 550 genes had a 10-fold greater difference in expression."}, {"asset": "source:pmid:23183685", "locator": "sections[6] \"5. Representative Results\" paragraph 2", "quote": "Figure 1 was generated for comparing expression profiles in three regions (striatum, parietal cortex and MAV) under control conditions using Agilent-014879 Whole Rat Genome 4x44K 60mer oligonucleotide arrays (G4131F, Agilent Technologies, Palo Alto, CA; NCBI GEO Accession # GPL7294; GSE23093 and GSE29733 that are present at the NCBI GEO repository)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using Agilent whole-rat genome oligonucleotide arrays and volcano plots, the study found that MAV gene expression was markedly distinct from striatum and parietal cortex, with the source expression data available through NCBI GEO under GSE23093 and GSE29733.", "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:23183685"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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"licence_read": false}}, {"id": "asset:table:pmid:23183685:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2910cccef9f8b4279a17b2b2f15a00126399a31b1bda0f583149305af3069bf1", "bytes": 3130, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#d36e274", "version": null, "note": null, "structure": {"pmcid": "PMC3523424", "section_index": 7, "section_title": "Abbreviations", "row_count": 22, "column_count": 3}, "table": {"label": null, "caption": null, "rows": [["MAV Expression Brain Expression", "NCBI Gene Symbols", "Tissue Specificity or Reported Function(s)"], ["> 50-fold", "Anxa2a, Col8a1, Des, Esm1, Glycam1, Kla, Lect1, Lepr, Lum, Myh11, Ogn, Tagln, Thbs2, Tnnt2", "Vasculature & Heart"], ["> 50-fold", "Ccl19, Cd74a, Defb1, Lrrc21, Mgl1, Mrc1, Msln, Pla2g5, Prg4, RT1-Bb, RT1-Da", "Immune System"], ["> 50-fold", "Adh1, Aebp1, Aldh1a2, Gstm2", "Retinoic Acid & Lipid Processing"], ["> 50-fold", "Cdh1, Col3a1, Col1a2, Colec12, Cpxm2, Cpz, Dcn, Emp3, Gpc3, Nupr1, Omd, Pcolce Slamf9, Tmem27, Tspan8", "Extracellular Matrix & cell-cell junctions"], ["> 50-fold", "Aqp1, Asgr1, Kcnj13, Slc5a5, Slc6a13, Slc6a20, Slc22a6, Sned1, Ttr", "Ion & Solute Homeostasis"], ["> 50-fold", "Alx3, Cdkn1c, Foxc2, Igfbp2, Ifitm1, Ifitm2, Nkx6-1, Osr1, Prrx2, Sfrp1, Tbx15. Upk1b, Wisp2, Wnt6", "Development & Transcription Regulation"], ["> 50-fold", "Gpha2, Mfap5, Mpzl2 Plac8, Scgb1c1, Sostdc1, Steap1", "Unknown & Miscellaneous"], ["30 to 50-fold", "Anxa1a , Angpt2, C6a, Gjb2, Ptgis, Thbd, Timp1", "Vasculature & Heart"], ["30 to 50-fold", "Casp12, Ccl2, Ccr1, Cd14, Cxcl10, Ifitm3, Klra5, Lgals1, Lgals3, Ms4a4a, Ms4a7, Plscr1, Spp1, Xcl1", "Immune System"], ["30 to 50-fold", "Col6a3, Cpxm1, Efemp1, Fmod, Mgp, Nid2", "Extracellular Matrix & cell-cell junctions"], ["30 to 50-fold", "Cp, Cubn, Gcgr, S100a6, Scn7a, Sct, Slc4a5, Slc16a11, Slco1a5", "Ion & Solute homeostasis"], ["30 to 50-fold", "Cfd, Ch25h, Crabp2, Rarres2", "Retinoic Acid & Lipid Processing"], ["30 to 50-fold", "Bmp6, Casp12, Dab2, Folr1, Igf2, Msx1, Tbx18, Twist1, Wnt5b", "Development & Transcription Regulation"], ["30 to 50-fold", "Cela3b, Cln6, C1qtnf7, Copz2, Dhrs7c, Gng11, Prss23, Srpx, Vim", "Unknown & Miscellaneous"], ["15 to 30-fold", "Adm, Angpt1, Angptl2, Bgn, Cklfa, Cnn1,Cox8h, Ctsk, F13a1, Gja5, Klf4, Lox, Lyz, Myl9, Procr, Pros1, RT1-Ba, Serpinb10, Serping1, Serpinf1, Tgm2, Tnmd, Trim63, Txnipa, Vamp5, Vtn", "Vasculature & Heart"], ["15 to 30-fold", "Adaa, Bst2, Ccl6, Cd40, Cd68, Ctsc, Dap, Faim3, Fkbp9, Fxyd5, Fmo1, Glipr1, Ier3, Ifi47, Igsf6, Msc, Nfatc4, RT1-Db1, Serpinb1a, Tir4, Tubb6", "Immune System"], ["15 to 30-fold", "Adamtsl4, Col1a1, Crb3, Dpt, Egfl3, Fbn1, Fbln1, Fbln5, Fn1, Itgb4, Lama2, Lgals3bp, Loxl1, Mfap4, Mmp14, Mmp23, Ppic, Serpinh1, Timp3", "Extracellular Matrix & cell-cell junctions"], ["15 to 30-fold", "Cybrd1, Selenbp1, Slc2a4, Slc9a2, Slc13a3, Slc16a4, Slc22a8, Slc22a18", "Ion & Solute homeostasis"], ["15 to 30-fold", "Agpat2, Bdh2, Cyp26b1, Lpar3, Ltb4dh, Olr1, Pon3, Rbp1, Rbp4", "Retinoic Acid & Lipid Processing"], ["15 to 30-fold", "Atf3, Dkk4, Eya2, Ifitm7, Ltbp1, Mustn1, Nr2f2, Ptrf, Sphk1, Tgfbi, Tcea3 Tcfap2b, Wnt2b, Wnt5a, Zic1", "Development & Transcription Regulation"], ["15 to 30-fold", "Adamts12, Adamtsl3, C1r, Crispld2, Crygn, Cyp1b1, Dse, Enpep, Enpp2, Epn3, Flna, Fmo3, Gnmt, Gprc5c, Hspb1, Klc3, Krt18, Krt19, Mdk, Mesp1, Ms4a6a, Ms4a6b, Ms4a11, Net1, Pdlim2, Phactr2, Plp2, Ppp1r3b, Pqlc3, Rin3, Spag11, Sult1a1, Tmem106a, Wfikkn2", "Unknown & Miscellaneous"]], "row_count": 22, "column_count": 3, "numeric_cells": 37, "header_rows": 0, "locator": "section[7]/table-wrap[1]#d36e274"}}], "gaps": ["asset:data:geo:GSE23093 not downloaded", "asset:data:geo:GSE23093 licence not read", "asset:data:geo:GSE29733 not downloaded", "asset:data:geo:GSE29733 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}