← All .science files
pmid:40875264
Early proteomic response in thyroid gland after 131I administration in female Balb/c mice.
Nils Rudqvist · Johan Spetz · Emil Schüler · Toshima Z Parris · Britta Langen · Carina Sihlbom Wallem · Khalil Helou · Eva Forssell-Aronsson
Radiation protection dosimetry · 2025 doi:10.1093/rpd/ncaf057
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 8 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[2] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40875264", "kind": "science-record", "revision": 2, "content_hash": "sha256:dfd89af6016112d6feeec2cea7d19751b2518e99e9a358ced5f43e855320ad44", "created_at": "2026-11-01T20:30:59Z", "updated_at": "2026-11-01T21:35:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Early proteomic response in thyroid gland after 131I administration in female Balb/c mice.", "doi": "10.1093/rpd/ncaf057", "pmid": "40875264", "authors": ["Nils Rudqvist", "Johan Spetz", "Emil Schüler", "Toshima Z Parris", "Britta Langen", "Carina Sihlbom Wallem", "Khalil Helou", "Eva Forssell-Aronsson"], "journal": "Radiation protection dosimetry", "year": 2025, "abstract": "131I (iodide) accumulates in the thyroid and may affect thyroid tissue. Mechanisms behind such effects are not known. The aim was to investigate early changes in protein expression in thyroid and plasma from mice injected with 131I as iodide. Female Balb/c nude mice were i.v. injected with 0 or 490 kBq 131I and killed after 24 h. Thyroid and blood samples were collected from each animal. Protein levels were determined by mass spectrometry. Data are available via ProteomeXchange with identifier PXD062861. Altogether, 17 and 20 proteins showed statistically significant altered levels in thyroid gland and plasma, respectively, after 131I exposure. Most of these proteins had decreased and increased levels in thyroid and plasma, respectively. Few of them were previously proposed radiation responsive proteins. Functional annotation suggests impact on haematopoiesis, reduced oxygen levels, and hypothyroidism. The role of CHIA and PGAM2 in radiation-induced response should be further examined, together with identification and validation of biomarkers of 131I exposure.", "claims": [{"id": "claim-method", "statement": "Statistical significance between treated and control group was determined using a Welch’s t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40875264", "locator": "sections[10] \"Database search for protein TMT quantification\" paragraph 2", "quote": "Statistical significance between treated and control group was determined using a Welch’s t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [28] partner repository with the dataset identifier PXD062861.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40875264", "locator": "sections[10] \"Database search for protein TMT quantification\" paragraph 3", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [28] partner repository with the dataset identifier PXD062861."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Altogether, 17 and 20 proteins showed statistically significant altered levels in thyroid gland and plasma, respectively, after 131I exposure.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40875264", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Altogether, 17 and 20 proteins showed statistically significant altered levels in thyroid gland and plasma, respectively, after 131I exposure."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Altogether, 17 and 20 proteins showed statistically significant altered levels in thyroid gland and plasma, respectively, after 131I exposure.", "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:40875264"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD062861"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD062861"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40875264", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1093/rpd/ncaf057", "sha256": "sha256:5ae76c6f9c20a988d84049b12c98a367c5f8e78e955ac17e53b23c429227675b", "bytes": 45233, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1093/rpd/ncaf057", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12392886", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD062861", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD062861", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD062861", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [28] partner repository with the dataset identifier PXD062861.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [28] partner repository with the dataset identifier PXD062861.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Early proteomic response in thyroid gland after I-131 administration in female Balb/c mice", "resolution_checked_at": "2026-11-01T20:16:18Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD062861 not downloaded", "asset:data:geo:PXD062861 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "welch_t_test", "label": "Group comparison", "dsl_operations": ["welch_t"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Statistical significance between treated and control group was determined using a Welch’s t-test."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["welch_t"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: welch_t_test."}, "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": ["PXD062861"], "resolved_accessions": ["PXD062861"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [28] partner repository with the dataset identifier PXD062861."], "basis": "The paper names PXD062861 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": ["welch_t"], "assets": ["source:pmid:40875264", "data:geo:PXD062861"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD062861"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:00:43Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12998, "completion_tokens": 1000, "cached_tokens": 256}}, "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:40875264", "type": "paper", "label": "pmid:40875264"}, {"id": "source:pmid:40875264", "type": "manuscript", "label": "PMID 40875264 full text"}, {"id": "data:geo:PXD062861", "type": "dataset", "label": "GEO PXD062861"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40875264", "type": "paper", "label": "pmid:40875264"}, {"id": "source:pmid:40875264", "type": "manuscript", "label": "PMID 40875264 full text"}, {"id": "data:geo:PXD062861", "type": "dataset", "label": "GEO PXD062861"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40875264", "type": "extraction", "used": ["source:pmid:40875264"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD062861", "type": "accession_resolution", "used": ["data:geo:PXD062861"], "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:40875264", "parent_hash": "sha256:f7b72d972702abcca50603393e406d62c0ed5f9c02e9e9f306c6e8960f931c49", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:PXD062861 licence not read", "asset:data:geo:PXD062861 not downloaded", "execution.not_run", "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": ["Early proteomic response in thyroid gland after 131I adminis", "ch animal. Protein levels were determined by mass spectrometry. Data are available via ProteomeXchange with"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["cted with 131I as iodide. Female Balb/c nude mice were i.v. injected with 0 or 490 kBq 131I and kil", "d libitum. At 24 h after administration, the mice were euthanized by cardiac puncture under anaesth"], "order_basis": "paper_text_order:308", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["welch_t"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Statistical significance between treated and control group was determined using a Welch’s t-test."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}