Seco-Duocarmycin SA in Aggressive Glioblastoma Cell Lines.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40141405", "kind": "science-record", "revision": 1, "content_hash": "sha256:412fecd546f321690638fa3ee0a2ecf1f6d3473644f6018282f4756ad47f138a", "created_at": "2026-11-01T10:25:50Z", "updated_at": "2026-11-01T10:25:50Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Seco-Duocarmycin SA in Aggressive Glioblastoma Cell Lines.", "doi": "10.3390/ijms26062766", "pmid": "40141405", "authors": null, "journal": "International journal of molecular sciences", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", "authors"]}, "experiment": 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"format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms26062766", "sha256": "sha256:f6acce6e87f070ec5e6bb23e118c7b4f78bcc9ff6dbdecf29b4059129dfa757c", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms26062766", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:40141405 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40141405"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40141405"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "e5e776552621a1108fd9e596f718907f4345dcb3278b8116bb94c6487c48eade", "source_hash": "f6acce6e87f070ec5e6bb23e118c7b4f78bcc9ff6dbdecf29b4059129dfa757c", "raw_response_sha256": "sha256:27bf777ced8670b64ea4118b20895c18eccbb7b12047344008e17c4a01fed4c5", "raw_response_chars": 3999}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "5603fb944341673acc2d2bed163ca1a9e92cbdaedc93da717c63be9a2bacce9a", "source_hash": "f6acce6e87f070ec5e6bb23e118c7b4f78bcc9ff6dbdecf29b4059129dfa757c", "raw_response_sha256": "sha256:94db6be9bf9c220e5ef67cebb02a8ac26bca1666c5002674664e1fbf08c44b99", "raw_response_chars": 58065}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "e217017ef79eff5e397f010f6a1920d7136e2384aac6785996451b3adcc319e7", "source_hash": "f6acce6e87f070ec5e6bb23e118c7b4f78bcc9ff6dbdecf29b4059129dfa757c", "raw_response": "{\"parent_value\":48,\"unit\":\"proteins\",\"evidence\":\"In response to seco-DSA treatment, the most substantial differentially expressed proteins were unique to the cell cycle (48 proteins), followed by autophagy (45 proteins), suggesting that these cellular processes play a significant role in the cytotoxicity of seco-DSA.\",\"target_result\":\"48 proteins\",\"number_stated\":true}", "reading": {"parent_value": 48, "unit": "proteins", "evidence": "In response to seco-DSA treatment, the most substantial differentially expressed proteins were unique to the cell cycle (48 proteins), followed by autophagy (45 proteins), suggesting that these cellular processes play a significant role in the cytotoxicity of seco-DSA.", "target_result": "48 proteins", "number_stated": true, "source_locator": "chars 2906-3175 of source sha256 f6acce6e87f070ec5e6bb23e118c7b4f78bcc9ff6dbdecf29b4059129dfa757c"}, "recorded_at": "2026-10-31T15:36:19.843355+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "9704ffddcbf6d603f18dc21ed62fe394e870bfd09c1cb0aa912aa5c8f14941c1", "source_hash": "f6acce6e87f070ec5e6bb23e118c7b4f78bcc9ff6dbdecf29b4059129dfa757c", "raw_response": "<think>We need answer JSON only. Need identify single numerical result headline numerical result paper states for main finding registered target. Source likely abstract says IC50 values lower but no exact values. Later proteomics numbers, 48 proteins etc. Need determine target likely headline numerical result for main finding. Maybe source text is partial, target wants numerical result paper itself states for registered target. Need extract exact contiguous quote with number. \"Furthermore, seco-DSA achieved its full cytotoxic effect within 8 h...\" Is 8 h headline numerical result main finding? Or proteomic finding \"most substantial ... cell cycle (48 proteins), followed by autophagy (45 proteins)\". Registered target phrased generic: \"the headline numerical result the paper states for its main finding\". We need infer from source. They ask \"single numerical result that a replication ... has to reproduce.\" Source has many numbers, but headline numerical likely perhaps 8 h. Need report number unit paper prints and quote clause whole attribution. Need think carefully.\n\nMaybe this is task from benchmark where source includes paper and target registered, perhaps target is an outcome from abstract, and ask exact number. We have title + abstract + sections. Main finding efficacy of seco-DSA in GBM cells. Abstract explicitly gives \"full cytotoxic effect within 8 h of drug incubation in GBM cell lines.\" That's likely headline numeric result. Proteomics analysis is supplemental and numerical counts 48 proteins etc, but likely not headline result. Registered target deliberately says \"the headline numerical result the paper states for its main finding\", perhaps requires selecting one number. The phrase \"headline numerical result\" could point to 8 h as main finding in abstract. Yet title perhaps no exact IC50 values, only lower than natural counterpart. Single headline numerical result = 8 h.\n\nLet's parse wording: \"Read the supplied paper text and find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed. The unit must be the unit the paper prints. The evidence must be an exact, contiguous quotation from SOURCE TEXT that contains the number; do not shorten it, do not add an ellipsis and do not paraphrase it. Attribution may be carried by the text's own wording: a number may be attached to the target by a parenthetical list, by the word 'respectively', or by words that name the target directly. When that is how the text links them, quote the whole clause so a reader can check the attribution for themselves. If the text states no number for the registered target, set number_stated to false, leave parent_value at 0, leave unit and evidence empty, and say in target_result what the text does state instead. Never invent a source.\"\n\nCould be a data extraction setup where target might refer to \"headline numerical result for main finding\". We need identify. In abstract: IC50 lower no values. Cell viability says sensitivity difference no numbers. Full cytotoxic effect within 8 h. This is only main finding with numerical value. Thus 8, unit \"h\" (paper prints \"8 h\"). Evidence exact contiguous quotation containing number, probably whole sentence: \"Furthermore, seco-DSA achieved its full cytotoxic effect within 8 h of drug incubation in GBM cell lines.\" target_result concise same. JSON valid, no markdown.\n\nNeed ensure number type 8, unit \"h\" not \"hours\" because unit paper prints is h. Evidence exact quote. target_result perhaps \"seco-DSA achieved its full cytotoxic effect within 8 h of drug incubation in GBM cell lines.\" Number stated true.\n\nBut let's not rush. Could headline numerical result refer to proteomics main finding: \"most substantial differentially expressed proteins were unique to the cell cycle (48 proteins), followed by autophagy (45 proteins)\". The main finding of paper perhaps mechanism due cell cycle disruption; in proteomics analysis, headline result 48 proteins. However title main finding may be cytotoxicity and mechanism. There is also dose 0.1 nM. Which is \"headline numerical result\"? Need infer likely evaluation expectations. Perhaps user wants \"single numerical result that a replication of registered target has to reproduce\" from article. The registered target isn't a named metric but generic descriptor. Maybe generated from a question like \"What was the IC50?\" Yet source omits actual IC50. They warn if no number, say false and what text states. Could be trick: abstract says IC50 values lower than natural DSA counterpart but no actual numbers; if registered target means headline numerical result perhaps maybe expected to find 8 h. Why include all these details? Let's understand source structure.\n\nTitle \"Seco-Duocarmycin SA in Aggressive Glioblastoma Cell Lines\". Abstract states:\n- efficacy seco-DSA novel DNA alkylating\n- colony assay IC50 values lower than natural DSA\n- cell viability LN18 more sensitive to DSA than T98G\n- full cytotoxic effect within 8 h\n- concentration-dependent apoptosis, not fully explain viability\n- significant cell cycle arrest S/G2/M\n- mechanism primarily disruption cell cycle\n- proteomic dysregulation proteins senescence apoptosis DNA repair\n- dataset ID.\n\nThen methods/proteomics findings. The \"headline numerical result\" in title/abstract is indeed 8 h. They might expect 8 h. The proteomic counts are not abstract's headline and section 2.7 perhaps from results but less central.\n\n\"Registered target: the headline numerical result the paper states for its main finding\" seems intentionally broad, perhaps an evaluator asks us to select a numerical result. Single numerical result likely a \"time to full cytotoxic effect\". A replication would reproduce 8 h. Use exact quote.\n\nCould parent_value perhaps 8.0? JSON number 8.\n\nNeed target_result not paraphrase? Only evidence exact quote constraints; target_result can concise. Could quote it as well. Ensure evidence exact, contiguous. Let's verify punctuation and Unicode: SOURCE: \"Furthermore, seco-DSA achieved its full cytotoxic effect within 8 h of drug incubation in GBM cell lines.\" Use curly apostrophe irrelevant. Exact.\n\nUnit perhaps \"h\" as printed. target_result perhaps \"Full cytotoxic effect within 8 h of drug incubation in GBM cell lines.\" This states result.\n\nReturn object only.</think>\n\n{\"parent_value\":8,\"unit\":\"h\",\"evidence\":\"Furthermore, seco-DSA achieved its full cytotoxic effect within 8 h of drug incubation in GBM cell lines.\",\"target_result\":\"Full cytotoxic effect within 8 h of drug incubation in GBM cell lines.\",\"number_stated\":true}", "reading": {"parent_value": 8, "unit": "h", "evidence": "Furthermore, seco-DSA achieved its full cytotoxic effect within 8 h of drug incubation in GBM cell lines.", "target_result": "Full cytotoxic effect within 8 h of drug incubation in GBM cell lines.", "number_stated": true, "source_locator": "chars 610-715 of source sha256 f6acce6e87f070ec5e6bb23e118c7b4f78bcc9ff6dbdecf29b4059129dfa757c"}, "recorded_at": "2026-10-31T15:36:27.139460+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "seco-DSA achieved its full cytotoxic effect within 8 h of drug incubation in GBM cell lines.", "minimax_alt": "In response to seco-DSA treatment, the most substantial differentially expressed proteins were unique to the cell cycle (48 proteins), followed by autophagy (45 proteins), suggesting that these cellular processes play a significant role in the cytotoxicity of seco-DSA.", "decisive": false}, "physical_methods": {"minimax": ["Colony formation assay", "Cell viability assay", "Apoptosis assay", "Flow cytometry with FxCycle PI/RNase staining", "LC-MS/MS proteomic analysis"], "minimax_alt": ["Protein isolation and LC-MS/MS proteomic analysis of treated and control LN18 cells", "Cell-cycle analysis by flow cytometry after FxCycleTM PI/RNase staining using a MACSQuant® Analyzer 10 cytometer", "Colony formation assay", "Cell viability assay"], "decisive": false}, "analysis_methods": {"minimax": ["Differential expression analysis using log-fold change relative to control peak intensity", "clusterProfiler biological processes ontology annotation", "UpSetR visualization", "Two-tailed unpaired t-test"], "minimax_alt": ["Differential expression analysis of LC-MS/MS peak-intensity data using Log-Fold Change values relative to control, with a baseline threshold of 2 LFC", "Biological-process ontology annotation of differentially expressed proteins using clusterProfiler in R version 4.4.1", "UpSet-plot visualization using UpSetR", "FlowJo software analysis of flow-cytometry cell-cycle data"], "decisive": false}, "statistical_method": {"minimax": "Two-tailed unpaired t-test", "minimax_alt": "", "decisive": true}, "parent_value": {"minimax": 48, "minimax_alt": 8, "decisive": true}, "unit": {"minimax": "proteins", "minimax_alt": "h", "decisive": true}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:04ea4e69abb23903d64ef29fdf14225d27527134f789f63b65da8be092b9e270", "type": "sep_package", "label": "SEP v1 package for pmid:40141405"}], "activities": [{"id": "activity:conversion:pmid:40141405", "type": "conversion", "used": ["package:04ea4e69abb23903d64ef29fdf14225d27527134f789f63b65da8be092b9e270"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "326c10b6-3e65-442b-9699-e7587aa3f12e", "parent_hash": "04ea4e69abb23903d64ef29fdf14225d27527134f789f63b65da8be092b9e270", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40141405 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40141405' does not resolve to a declared asset", "targets"]}