{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34287056", "kind": "science-record", "revision": 6, "content_hash": "sha256:218dcc147b876d278115ca1d5e7699023234de9fc6f922a8faba92eb17033dbf", "created_at": "2026-11-01T15:41:44Z", "updated_at": "2026-11-01T21:25:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Actin Filament-Associated Proteins in Giardia lamblia.", "doi": "10.1128/Spectrum.00558-21", "pmid": "34287056", "authors": ["Melissa C Steele-Ogus", "Richard S Johnson", "Michael J MacCoss", "Alexander R Paredez"], "journal": "Microbiology spectrum", "year": 2021, "abstract": "The deep-branching protozoan parasite Giardia lamblia is the causative agent of the intestinal disease giardiasis. Consistent with its proposed evolutionary position, many pathways are minimalistic or divergent, including its actin cytoskeleton. Giardia is the only eukaryote known to lack all canonical actin-binding proteins. Previously, our lab identified a number of noncanonical Giardia lamblia actin (GlActin) interactors; however, these proteins appeared to interact only with monomeric or globular actin (G-actin) rather than with filamentous actin (F-actin). To identify F-actin interactors, we used a chemical cross-linker to preserve native interactions followed by an anti-GlActin antibody, protein A affinity chromatography, and liquid chromatography coupled to mass spectrometry. We found 46 putative actin interactors enriched under the conditions favoring F-actin. Data are available via ProteomeXchange with identifier PXD026067. None of the proteins identified contain known actin-interacting motifs, and many lacked conserved domains. Each potential interactor was then tagged with the fluorescent protein mNeonGreen and visualized in live cells. We categorized the proteins based on their primary localization; localizations included ventral disc, marginal plate, nuclei, flagella, plasma membrane, and internal membranes. One protein from each of the six categories was colocalized with GlActin using immunofluorescence microscopy. We also co-immunoprecipitated one protein from each category and confirmed three of the six potential interactions. Most of the localization patterns are consistent with previously demonstrated GlActin functions, but the ventral disc represents a new category of actin interactor localization. These results suggest a role for GlActin in ventral disc function, which has previously been controversial. IMPORTANCE Giardia lamblia is an intestinal parasite that colonizes the small intestine and causes diarrhea, which can lead to dehydration and malnutrition. Giardia actin (GlActin) has a conserved role in Giardia cells, despite being a highly divergent protein with none of the conserved regulators found in model organisms. Here, we identify and localize 46 interactors of polymerized actin. These putative interactors localize to a number of places in the cell, underlining GlActin's importance in multiple cellular processes. Surprisingly, eight of these proteins localize to the ventral disc, Giardia's host attachment organelle. Since host attachment is required for infection, proteins involved in this process are an appealing target for new drugs. While treatments for Giardia exist, drug resistance is becoming more common, resulting in a need for new treatments. Giardia and human systems are highly dissimilar, thus drugs specifically tailored to Giardia proteins would be less likely to have side effects.", "claims": [{"id": "claim-method", "statement": "False discovery rates (1%) were determined using PeptideProphet (75), and protein inferences were made using ProteinProphet (76).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34287056", "locator": "sections[16] \"Liquid chromatography and mass spectrometry.\" paragraph 3", "quote": "False discovery rates (1%) were determined using PeptideProphet (75), and protein inferences were made using ProteinProphet (76)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data were deposited to the ProteomeXchange (80) Consortium via the PRIDE partner repository with the data set identifier PXD026067 (81).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34287056", "locator": "sections[22] \"Data availability.\" paragraph 2", "quote": "The mass spectrometry proteomics data were deposited to the ProteomeXchange (80) Consortium via the PRIDE partner repository with the data set identifier PXD026067 (81)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:34287056"], "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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"open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tab1", "version": null, "note": "Proteins identified as putative F-actin interactorsa", "structure": {"pmcid": "PMC8552679", "section_index": 3, "section_title": "Identification of noncanonical GlActin interactors.", "row_count": 54, "column_count": 3}, "table": {"label": "TABLE 1", "caption": "Proteins identified as putative F-actin interactorsa", "rows": [["ORF no.", "Identity", "Localization"], ["Plasma membrane/cortical localization", "", ""], ["GL50803_8560", "Hypothetical", "Plasma membrane"], ["GL50803_103855", "VPS29", "Plasma membrane"], ["GL50803_23833", "VPS35", "Plasma membrane"], ["GL50803_4259", "Clathrin light chain", "Plasma membrane"], ["GL50803_8044", "7 transmembrane domains", "Plasma membrane and unidentified compartment"], ["GL50803_15591", "Coiled-coil protein", "Plasma membrane"], ["GL50803_14551", "Alpha-6 giardin", "Ventrolateral flange and plasma membrane"], ["GL50803_17255", "Hypothetical", "Plasma membrane, flange, basal bodies"], ["GL50803_5810", "Hypothetical", "Plasma membrane"], ["GL50803_11684", "Leucine-rich repeat protein", "Plasma membrane"], ["Internal membrane localization", "", ""], ["GL50803_9861", "Hypothetical", "Diffuse internal membrane"], ["GL50803_13930", "Arf3", "Puncta"], ["GL50803_22855", "Hypothetical", "Vesicles"], ["GL50803_12999", "Hypothetical", "Puncta and unidentified compartment"], ["Marginal plate localization", "", ""], ["GL50803_17153", "Alpha-11 giardin", "Marginal plate and axonemal-associated structures"], ["GL50803_115478", "Ankyrin repeat, takusan, SMC", "Marginal plate and flagellar exit sites"], ["GL50803_8854", "Hypothetical", "Marginal plate and flagellar exit sites"], ["GL50803_4383", "Ankyrin repeat", "Marginal plate and axonemal-associated structures"], ["GL50803_5800", "Hypothetical", "Marginal plate and puncta"], ["GL50803_9030", "Ankyrin repeat", "Marginal plate and cytoplasmic puncta"], ["GL50803_16522", "Hypothetical", "Cytoplasmic, marginal disc, nuclei"], ["Nuclear localization", "", ""], ["GL50803_101212", "Hypothetical", "Perinuclear region"], ["GL50803_33989", "Hypothetical", "Puncta and filaments within nucleus"], ["GL50903_14299", "Hypothetical", "Diffuse nuclear localization with puncta"], ["GL50803_5328", "Sigma adaptin (AP-2 complex)", "Diffuse nuclear localization and plasma membrane"], ["GL50803_102813", "Ankyrin repeat", "Nuclear, marginal plate, cytoplasmic"], ["GL50803_14213", "Hypothetical", "Diffuse nuclear localization with puncta"], ["Flagellar localization", "", ""], ["GL50803_9848", "Dynein light chain", "Internal portions of flagella, basal bodies"], ["GL50803_33685", "Armadillo repeat", "Flagella"], ["GL50803_15097", "Alpha-14 giardin", "Flagella"], ["GL50803_13774", "Hypothetical", "Flagellar exit sites"], ["GL50803_4463", "Dynein light chain", "Flagella"], ["GL50803_15124", "Dynein light chain", "Flagella"], ["Disc localization", "", ""], ["GL50803_4239", "Hypothetical", "Ventral disc, cytoplasmic"], ["GL50803_24451", "FGF", "Flagella, basal bodies, lateral crest"], ["GL50803_8726", "Hypothetical", "Ventral disc, midbody"], ["GL50803_27925", "Ankyrin repeat", "Ventral disc, except ventral groove"], ["GL50803_113622", "Ankyrin repeat", "Ventral groove"], ["GL50803_16844", "Hypothetical", "Ventral disc: ventral groove and overlap zone"], ["GL50803_17230", "Gamma-giardin", "Ventral disc"], ["GL50803_11354", "Hypothetical", "Flagella, lateral crest"], ["Nonspecific localization", "", ""], ["GL50803_10038", "Alpha-18 giardin", "Diffuse nonspecific"], ["GL50803_10429", "Wos2 protein", "Diffuse nonspecific"], ["GL50803_7323", "Hypothetical", "Diffuse nonspecific"], ["GL50803_6242", "Translationally controlled tumor protein-like", "Diffuse nonspecific"], ["GL50803_21423", "Beta-adaptin", "NA"]], "row_count": 54, "column_count": 3, "numeric_cells": 54, "header_rows": 1, "locator": 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:34287056", "data:geo:PXD026067", "asset:table:pmid:34287056:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD026067"]}, "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": "2026-10-31T18:32:46Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 58265, "completion_tokens": 1000, "cached_tokens": 19584}}, "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:34287056", "type": "paper", "label": "pmid:34287056"}, {"id": "source:pmid:34287056", "type": "manuscript", "label": "PMID 34287056 full text"}, {"id": "data:geo:PXD026067", "type": "dataset", "label": "GEO PXD026067"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34287056", "type": "paper", "label": "pmid:34287056"}, {"id": "source:pmid:34287056", "type": "manuscript", "label": "PMID 34287056 full text"}, {"id": "data:geo:PXD026067", "type": "dataset", "label": "GEO PXD026067"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34287056", "type": "extraction", "used": ["source:pmid:34287056"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD026067", "type": "accession_resolution", "used": ["data:geo:PXD026067"], "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:34287056", "parent_hash": "sha256:658af458eb20802a9854a502c26445eb464b7a871241f9c808830555710b0343", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD026067 licence not read", "asset:data:geo:PXD026067 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": ["graphy, and liquid chromatography coupled to mass spectrometry. We found 46 putative actin interactors enri", "HODS Purification and sample preparation for mass spectrometry. Lysates were incubated overnight with an an", "digestion. Supernatant was then removed for LC-MS/MS analysis. Protein was further extracted from", "esuspended in solvent A and then analyzed by LC-MS/MS as described below. Supplementary Materials"], "order_basis": "paper_text_order:803", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ategories was colocalized with GlActin using immunofluorescence microscopy. We also co-immunoprecipitated on"], "order_basis": "paper_text_order:1450", "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":"2026-11-04T03:38:26+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}}}