{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30390017", "kind": "science-record", "revision": 7, "content_hash": "sha256:a393105f1922f337f961cab38b6c48885006833712bb3dae88e8c4037ead5d69", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T22:00:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomics based analysis of the nicotine catabolism in Paenarthrobacter nicotinovorans pAO1.", "doi": "10.1038/s41598-018-34687-y", "pmid": "30390017", "authors": ["Marius Mihăşan", "Cornelia Babii", "Roshanak Aslebagh", "Devika Channaveerappa", "Emmalyn Dupree", "Costel C Darie"], "journal": "Scientific reports", "year": 2018, "abstract": "Paenarthrobacter nicotinovorans is a nicotine-degrading microorganism that shows a promising biotechnological potential for the production of compounds with industrial and pharmaceutical importance. Its ability to use nicotine was linked to the presence of the catabolic megaplasmid pAO1. Although extensive work has been performed on the molecular biology of nicotine degradation in this bacterium, only half of the genes putatively involved have been experimentally linked to nicotine. In the current approach, we used nanoLC-MS/MS to identify a total of 801 proteins grouped in 511 non-redundant protein clusters when P. nicotinovorans was grown on citrate, nicotine and nicotine and citrate as the only carbon sources. The differences in protein abundance showed that deamination is preferred when citrate is present. Several putative genes from the pAO1 megaplasmid have been shown to have a nicotine-dependent expression, including a hypothetical polyketide cyclase. We hypothesize that the enzyme would hydrolyze the N1-C6 bond from the pyridine ring with the formation of α-keto- glutaramate. Two chromosomally-encoded proteins, a malate dehydrogenase, and a D-3-phosphoglycerate dehydrogenase were shown to be strongly up-regulated when nicotine was the sole carbon source and could be related to the production the α-keto-glutarate. The data have been deposited to the ProteomeXchange with identifier PXD008756.", "claims": [{"id": "claim-method", "statement": "Significance was assessed using the Fisher’s Exact test and the p-values were further adjusted using the Benjamini and Hochberg correction to account for multiple comparisons30.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30390017", "locator": "sections[13] \"Data analysis\" paragraph 4", "quote": "Significance was assessed using the Fisher’s Exact test and the p-values were further adjusted using the Benjamini and Hochberg correction to account for multiple comparisons30."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the MassIVE partner repository with the dataset identifier PXD008756.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30390017", "locator": "sections[18] \"Availability of Materials and Data\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the MassIVE partner repository with the dataset identifier PXD008756."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:30390017"], "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": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. 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"268", "482"], ["Specific to P. nicotinovorans", "—", "66", "85", "62", "115"], ["pAO1 megaplasmid", "175", "1", "21", "27", "28"], ["Total number of non-redundant proteins", "—", "398", "391", "279", "511"]], "row_count": 7, "column_count": 6, "numeric_cells": 23, "header_rows": 2, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:30390017:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8e5b0f7e6398ac2268e302af3001661ac4e654418f86c2e183f438e754157273", "bytes": 2879, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#Tab2", "version": null, "note": "Differentially regulated pAO1-encoded proteins during the growth of Paenarthrobacter nicotinovorans on different carbon sources.", "structure": {"pmcid": "PMC6214936", "section_index": 4, "section_title": "Differentially regulated plasmid-encoded proteins in P. nicotinovorans in the presence of nicotine", "row_count": 22, "column_count": 9}, "table": {"label": "Table 2", "caption": "Differentially regulated pAO1-encoded proteins during the growth of Paenarthrobacter nicotinovorans on different carbon sources.", "rows": [["", "Protein", "UniProt ID", "Compared growth conditions"], ["Nicotine vs Citrate", "Nicotine and Citrate vs Citrate", "Nicotine vs Nicotine and Citrate"], ["Fold Change", "Fisher’s exact test (p < 0.00245)", "Fold Change", "Fisher’s exact test (p < 0.00077)", "Fold Change", "Fisher’s exact test (p < 0.00249)"], ["1", "2,6-dihydropseudooxynicotine hydrolase, DHPONH", "DHPON_PAENI", "INF", "<0.00010", "INF", "<0.00010", "3", "<0.00010"], ["2", "2,6-dihydroxypyridine 3-monooxygenase, DHPH", "DHPH_PAENI", "INF", "<0.00010", "INF", "<0.00010", "2.8", "<0.00010"], ["3", "2-oxoglutaramate amidase, NIT", "NIT_PAENI", "INF", "<0.00010", "INF", "<0.00010", "2.3", "0.011"], ["4", "4-methylaminobutanoate oxidase (formaldehyde-forming), MABO", "MABO1_PAENI", "INF", "0.00013", "n.d", "—", "INF", "<0.00010"], ["5", "4-methylaminobutanoate oxidase (methylamine-forming), MAO", "MABO2_PAENI", "INF", "<0.00010", "INF", "<0.00010", "3.9", "<0.00010"], ["6", "6-hydroxy-L-nicotine oxidase 6-HLNO", "Q93NH4_PAENI", "INF", "<0.00010", "INF", "0.00029", "27", "<0.00010"], ["7", "6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha, KDHA", "KDHA_PAENI", "INF", "<0.00010", "INF", "<0.00010", "4.2", "<0.00010"], ["8", "Bifunctional protein FolD", "Q8GAI4_PAENI", "INF", "0.00069", "n.d", "—", "INF", "0.0002"], ["9", "Formyltetrahydrofolate deformylase, PurU", "Q8GAI2_PAENI", "INF", "0.0017", "n.d", "—", "INF", "0.0014"], ["10", "Hypothetical polyketide cyclase, PKC", "Q93NG4_PAENI", "INF", "<0.00010", "INF", "<0.00010", "1.4", "0.15"], ["11", "NAD(P)H-Nicotine Blue (4,4′,5,5′-tetrahydroxy-3,3′-diazadiphenoquinone-(2,2′)) Oxidoreductase, NBOR", "Q8GAJ2_PAENI", "INF", "<0.00010", "INF", "<0.00010", "1.4", "0.23"], ["12", "Nicotine dehydrogenase large subunit NDHL", "Q93NH5_PAENI", "INF", "<0.00010", "INF", "0.00031", "3.1", "0.0058"], ["13", "Nicotine dehydrogenase medium subunit, NDHM", "Q59127_PAENI", "INF", "<0.00010", "INF", "<0.00010", "2.7", "0.0078"], ["14", "Nicotine dehydrogenase small subunit, NDHS", "Q59129_PAENI", "INF", "<0.00010", "INF", "0.00031", "3.1", "0.0058"], ["15", "ORF106, putative molybdenum transport ATPase, MODC", "Q93NG5_PAENI", "INF", "0.0011", "INF", "<0.00010", "1.5", "0.25"], ["16", "ORF78, putative carbon monoxide dehydrogenase subunit G, COXG", "Q93NG2_PAENI", "INF", "<0.00010", "INF", "<0.00010", "2", "0.00017"], ["17", "ORF76, putative carbon monoxide dehydrogenase subunit D, COXD", "Q93NG0_PAENI", "INF", "<0.00010", "INF", "<0.00010", "1.5", "0.24"], ["18", "Succinate-semialdehyde dehydrogenase SsaDH", "SSDH_PAENI", "INF", "<0.00010", "INF", "0.00023", "7.4", "0.00013"], ["19", "ORF92, hypothetical DUF948 domain-containing protein", "Q8GAH6_PAENI", "INF", "0.00032", 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p-values were further adjusted using the Benjamini and Hochberg correction to account for multiple comparisons30."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: blast."}, "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": "R4", "reachable": false, "accessions": ["PXD008756"], "resolved_accessions": [], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the MassIVE partner repository with the dataset identifier PXD008756."], "basis": "The paper names PXD008756, but the accession does not resolve in the repository (not_in_proteomexchange), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["sequence_align", "alignment_identity"], "assets": ["source:pmid:30390017", "data:geo:PXD008756", "asset:table:pmid:30390017:1", "asset:table:pmid:30390017:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD008756"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:46Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 32246, "completion_tokens": 953, "cached_tokens": 793}}, "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:30390017", "type": "paper", "label": "pmid:30390017"}, {"id": "source:pmid:30390017", "type": "manuscript", "label": "PMID 30390017 full text"}, {"id": "data:geo:PXD008756", "type": "dataset", "label": "GEO PXD008756"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30390017", "type": "paper", "label": "pmid:30390017"}, {"id": "source:pmid:30390017", "type": "manuscript", "label": "PMID 30390017 full text"}, {"id": "data:geo:PXD008756", "type": "dataset", "label": "GEO PXD008756"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30390017", "type": "extraction", "used": ["source:pmid:30390017"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD008756", "type": "accession_resolution", "used": ["data:geo:PXD008756"], "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:30390017", "parent_hash": "sha256:aa27a2fb8903ddff78abae5fab4e5f4398ca9200ae82170542397bdc794ebb55", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD008756 licence not read", "asset:data:geo:PXD008756 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_unresolved"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Proteomics based analysis of the nicotine catabolism in", "of Materials and Data The mass spectrometry proteomics data have been deposited to the ProteomeXcha", "le 2. Availability of Materials and Data The mass spectrometry proteomics data have been deposited to the P"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["BLAST"], "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":"2026-11-04T02:53:50+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}}}