{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28419154", "kind": "science-record", "revision": 6, "content_hash": "sha256:245195a9e4de505e2a9e241a916d1917658130614179d45121181f7ebb2ffe80", "created_at": "2026-11-01T15:40:25Z", "updated_at": "2026-11-01T21:20:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Salt stress induces changes in the proteomic profile of micropropagated sugarcane shoots.", "doi": "10.1371/journal.pone.0176076", "pmid": "28419154", "authors": ["Lucas Z Passamani", "Roberta R Barbosa", "Ricardo S Reis", "Angelo S Heringer", "Patricia L Rangel", "Claudete Santa-Catarina", "Clícia Grativol", "Carlos F M Veiga", "Gonçalo A Souza-Filho", "Vanildo Silveira"], "journal": "PloS one", "year": 2017, "abstract": "Salt stress is one of the most common stresses in agricultural regions worldwide. In particular, sugarcane is affected by salt stress conditions, and no sugarcane cultivar presently show high productivity accompanied by a tolerance to salt stress. Proteomic analysis allows elucidation of the important pathways involved in responses to various abiotic stresses at the biochemical and molecular levels. Thus, this study aimed to analyse the proteomic effects of salt stress in micropropagated shoots of two sugarcane cultivars (CB38-22 and RB855536) using a label-free proteomic approach. The mass spectrometry proteomics data are available via ProteomeXchange with identifier PXD006075. The RB855536 cultivar is more tolerant to salt stress than CB38-22. A quantitative label-free shotgun proteomic analysis identified 1172 non-redundant proteins, and 1160 of these were observed in both cultivars in the presence or absence of NaCl. Compared with CB38-22, the RB855536 cultivar showed a greater abundance of proteins involved in non-enzymatic antioxidant mechanisms, ion transport, and photosynthesis. Some proteins, such as calcium-dependent protein kinase, photosystem I, phospholipase D, and glyceraldehyde-3-phosphate dehydrogenase, were more abundant in the RB855536 cultivar under salt stress. Our results provide new insights into the response of sugarcane to salt stress, and the changes in the abundance of these proteins might be important for the acquisition of ionic and osmotic homeostasis during exposure to salt stress.", "claims": [{"id": "claim-method", "statement": "The same letter above the bars indicates no significant difference according to Tukey’s test at 5% probability.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28419154", "locator": "sections[10] \"Results\" paragraph 3", "quote": "The same letter above the bars indicates no significant difference according to Tukey’s test at 5% probability."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data are available via ProteomeXchange with identifier PXD006075.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28419154", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The mass spectrometry proteomics data are available via ProteomeXchange with identifier PXD006075."}], "state": "complete"}, {"id": "claim-target-result", "statement": "RB855536 exhibited greater salt tolerance than CB38-22; significance was assessed using Tukey’s test at 5% probability, and the mass-spectrometry proteomics source data are available via ProteomeXchange under identifier PXD006075.", "kind": "quantitative", "target": {"value": 5.0, "unit": "per cent", "tolerance": null, "source": "The same letter above the bars indicates no significant difference according to Tukey’s test at 5% probability."}, "evidence": [{"asset": "source:pmid:28419154", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The RB855536 cultivar is more tolerant to salt stress than CB38-22."}, {"asset": "source:pmid:28419154", "locator": "sections[10] \"Results\" paragraph 3", "quote": "The same letter above the bars indicates no significant difference according to Tukey’s test at 5% probability."}, {"asset": "source:pmid:28419154", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The mass spectrometry proteomics data are available via ProteomeXchange with identifier PXD006075."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "RB855536 exhibited greater salt tolerance than CB38-22; significance was assessed using Tukey’s test at 5% probability, and the mass-spectrometry proteomics source data are available via ProteomeXchange under identifier PXD006075.", "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:28419154"], "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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"section[10]/table-wrap[1]#pone.0176076.t001", "version": null, "note": "Proteins that were up-regulated or down-regulated under salt stress compared with their respective controls (CB-180/CB-0; RB-180/RB-0*) and proteins showing differential regulation between the two cultivars (RB-180/CB-180).", "structure": {"pmcid": "PMC5395195", "section_index": 10, "section_title": "Results", "row_count": 25, "column_count": 11}, "table": {"label": "Table 1", "caption": "Proteins that were up-regulated or down-regulated under salt stress compared with their respective controls (CB-180/CB-0; RB-180/RB-0*) and proteins showing differential regulation between the two cultivars (RB-180/CB-180).", "rows": [["Accession", "PeptideCount", "Score", "Log2_FC", "Relative abundance regulation", "Description", "Function"], ["CB-180/CB-0", "RB-180/RB-0", "RB-180/CB-180", "CB-180/CB-0", "RB-180/RB-0", "RB-180/CB-180"], ["Sb03g004560.1", "2", "15.1", "-1.859", "0.599", "0.774", "DOWN", "UP", "UP", "Photosystem I 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["Sb09g001600.1", "13", "144.5", "Unique CB-180", "1.044", "6.657", "Unique CB-180", "UP", "UP", "Glyceraldehyde-3-phosphate dehydrogenase C2", "Glycolytic process, carbohydrate metabolic process"], ["Sb03g011460.1", "2", "10.5", "Unique CB-180", "1.395", "0.828", "Unique CB-180", "UP", "UP", "Coatomer, beta subunit", "Intracellular protein transport"], ["Sb03g025720.1", "1", "5.6", "Unique CB-180", "2.106", "2.665", "Unique CB-180", "UP", "UP", "Carbamoyl phosphate synthetase B", "Urea cycle, arginine biosynthetic process"], ["Sb05g004860.1", "1", "7.1", "Unique CB-180", "4.399", "2.656", "Unique CB-180", "UP", "UP", "Cleavage stimulating factor 64", "Regulation of gene silencing, gene silencing by RNA"], ["Sb01g037950.1", "3", "18.7", "1.897", "0.823", "1.157", "UP", "UP", "UP", "Pathogenesis-related Bet v I family protein, putative, expressed", "Defence response, response to biotic stimulus"], ["Sb02g042550.1", "3", "18.1", "0.777", "0.928", "0.775", "UP", "UP", "UP", "Rubber elongation factor protein (REF)", "Translation elongation factor activity"], ["Sb03g028020.1", "6", "36.7", "0.514", "0.936", "0.586", "UP", "UP", "UP", "Oxidoreductase, aldo/keto reductase family protein, putative, expressed", "Starch biosynthetic process, maltose metabolic process"], ["Sb03g000850.1", "2", "22.4", "0.847", "1.031", "0.720", "UP", "UP", "UP", "Phosphorylase superfamily protein", "Nucleoside metabolic process"], ["Sb09g030530.1", "1", "5.7", "3.083", "1.266", "0.845", "UP", "UP", "UP", "Hypersensitive-induced response protein, putative, expressed", "Cellular cation homeostasis, regulation of plant-type hypersensitive response"], ["Sb08g014910.1", "2", "13.0", "3.116", "1.389", "2.578", "UP", "UP", "UP", "Calcium-dependent protein kinase 1", "Protein phosphorylation, intracellular signal transduction, abscisic acid-activated signalling pathway"], ["Sb03g032760.1", "3", "17.9", "1.435", "0.661", "2.140", "UP", "UP", "UP", "Myosin family protein with the Dil domain", "Actin filament-based movement"], ["Sb09g004430.1", "2", "10.3", "1.318", "1.473", "1.687", "UP", "UP", "UP", "Dihydrolipoyl dehydrogenase, putative, expressed", "Cell redox homeostasis, response to cadmium ion"], ["Sb10g023630.1", "6", "34.7", "1.543", "1.655", "1.071", "UP", "UP", "UP", "Phospholipase D alpha 1", "Lipid catabolic process, response to abscisic acid, regulation of stomatal movement"], ["Sb04g029040.2", "5", "29.8", "0.526", "1.663", "1.065", "UP", "UP", "UP", "Aldehyde dehydrogenase 2B7", "Aldehyde dehydrogenase (NAD) activity"], ["Sb04g027630.1", "3", "26.2", "4.756", "2.095", "2.025", "UP", "UP", "UP", "Lipase/lipoxygenase, PLAT/LH2 family protein", "Jasmonic acid biosynthetic process, response to wounding"], ["Sb06g017820.1", "1", "5.6", "0.645", "2.209", "0.829", "UP", "UP", "UP", "Translation initiation factor 2, small GTP-binding protein", "Protein biosynthesis, initiation factor"]], "row_count": 25, "column_count": 11, "numeric_cells": 158, "header_rows": 2, 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No tolerance is published because the paper states none."}], "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": "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 (Tukey’s test at 5% probability), 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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD006075"], "resolved_accessions": ["PXD006075"], "statements": ["The mass spectrometry proteomics data are available via ProteomeXchange with identifier PXD006075."], "basis": "The paper names PXD006075 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:28419154", "data:geo:PXD006075", "asset:table:pmid:28419154:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD006075"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:30:55Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 128274, "completion_tokens": 3104, "cached_tokens": 1560}}, "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:28419154", "type": "paper", "label": "pmid:28419154"}, {"id": "source:pmid:28419154", "type": "manuscript", "label": "PMID 28419154 full text"}, {"id": "data:geo:PXD006075", "type": "dataset", "label": "GEO PXD006075"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28419154", "type": "paper", "label": "pmid:28419154"}, {"id": "source:pmid:28419154", "type": "manuscript", "label": "PMID 28419154 full text"}, {"id": "data:geo:PXD006075", "type": "dataset", "label": "GEO PXD006075"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28419154", "type": "extraction", "used": ["source:pmid:28419154"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD006075", "type": "accession_resolution", "used": ["data:geo:PXD006075"], "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:28419154", "parent_hash": "sha256:0fc33a5fe243bbb0428f1b89d4363025120ce56c12f5d1b5653cbac3156a349f", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD006075 licence not read", "asset:data:geo:PXD006075 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ultivars CB38-22 and RB855536, respectively, cultured with 180 mM NaCl.(TIF)Click here for additional d"], "order_basis": "paper_text_order:5173", "id": "assay:1"}]},"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":"2026-11-04T02:14:52+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}}}