HER2-positive breast cancer with invasive micropapillary carcinoma component shows immunosuppressive microenvironment and resistance to neoadjuvant therapy.

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null, "source": "chars 1378-1500 of source sha256 670d0f3c400a9ec12fb132f47497827e1c8a2a6491abae3fa5b9d9322491647c"}, "evidence": [{"asset": "source:pmid:40821778", "locator": "chars 1378-1500 of source sha256 670d0f3c400a9ec12fb132f47497827e1c8a2a6491abae3fa5b9d9322491647c", "quote": "The IMPC group exhibited significantly lower pCR rates compared to the non-IMPC group: 21.6% vs. 47.1% (P = 0.004) overall"}]}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40821778"], "outputs": ["the published estimate, its unit and its interval"], 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"jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6339ba42bbb813ada8b6205800990e40a75b71c395a70157c0d26a996171d11e", "bytes": 1483, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T1", "version": null, "note": "Baseline characteristics.", "structure": {"pmcid": "PMC12354535", "section_index": 9, "section_title": "Baseline characteristics", "row_count": 26, "column_count": 5}, "table": {"label": "Table 1", "caption": "Baseline characteristics.", "rows": [["Characteristic", "Total (n = 244)", "IMPC (n = 38)", "Non-IMPC (n = 206)", "aP-value"], ["Median age (year)", "46 (25–74)", "44 (25–66)", "47 (25–74)", "0.133"], ["Age, n (%)", "", "", "", "0.183"], ["≤40", "80 (32.8)", "16 (42.1)", "64 (31.1)", ""], [">40", "164 (67.2)", "22 (57.9)", "142 (68.9)", ""], ["Tumor size, n (%)", "", "", "", "0.748"], ["≤ 2 cm", "20 (8.2)", "2 (5.3)", "18 (8.7)", ""], ["> 2 cm", "224 (91.8)", "36 (94.7)", "188 (91.3)", ""], ["Lymph nodes, n (%)", "", "", "", "0.406"], ["Negative", "12 (4.9)", "3 (7.9)", "9 (4.4)", ""], ["Positive", "232 (95.1)", "35 (92.1)", "197 (95.6)", ""], ["Hormone receptor, n (%)", "", "", "", "<0.05"], ["Negative", "90 (36.9)", "11 (28.9)", "79 (38.3)", ""], ["Positive", "154 (63.1)", "27 (71.1)", "127 (61.7)", ""], ["Grade, n (%)", "", "", "", "0.993"], ["G1 + G2", "135 (55.3)", "21 (55.3)", "114 (55.3)", ""], ["G3", "109 (44.7)", "17 (44.7)", "92 (44.7)", ""], ["Ki-67, n (%)", "", "", "", "0.254"], ["≤30%", "104 (42.6)", "13 (34.2)", "91 (44.2)", ""], [">30%", "140 (57.4)", "25 (65.8)", "115 (55.8)", ""], ["Neoadjuvant targeted therapy, n (%)", "", "", "", "0.052"], ["Trastuzumab", "94 (38.5)", "20 (52.6)", "74 (35.9)", ""], ["Trastuzumab + pertuzumab", "150 (61.5)", "18 (47.4)", "132 (64.1)", ""], ["Neoadjuvant chemotherapy, n (%)"], ["AC-T", "170 (69.7)", "24 (63.2)", "146 (70.9)", "0.342"], ["TCb", "74 (30.3)", "14 (35.8)", "60 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"1459cb735852eefdaee36ec1de2ab4851bce10ed2ef4bab1bd35f12ee83262ba", "source_hash": "670d0f3c400a9ec12fb132f47497827e1c8a2a6491abae3fa5b9d9322491647c", "raw_response_sha256": "sha256:9d9e740a46f8f9dc42017db9809ded461bceb6928fdc63fefc67f412192a5e5d", "raw_response_chars": 4637}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "fc63ba2c1031fa2a15e156732a8d6c53114f0f6c8faf0b913c82ee20a14e8ddf", "source_hash": "670d0f3c400a9ec12fb132f47497827e1c8a2a6491abae3fa5b9d9322491647c", "raw_response_sha256": "sha256:95a80186db95a3d58ae49cef443e58838babac9577f53f2d3a34767fe71f8877", "raw_response_chars": 76573}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "541e969952070f47ba86b0a0b91cc993f56080e6943aa831faa8fb4e3a823e36", "source_hash": "670d0f3c400a9ec12fb132f47497827e1c8a2a6491abae3fa5b9d9322491647c", "raw_response": "{\"parent_value\":21.6,\"unit\":\"%\",\"evidence\":\"The IMPC group exhibited significantly lower pCR rates compared to the non-IMPC group: 21.6% vs. 47.1% (P = 0.004) overall\",\"target_result\":\"Overall pathological complete response (pCR) rate in the IMPC group\",\"number_stated\":true}", "reading": {"parent_value": 21.6, "unit": "%", "evidence": "The IMPC group exhibited significantly lower pCR rates compared to the non-IMPC group: 21.6% vs. 47.1% (P = 0.004) overall", "target_result": "Overall pathological complete response (pCR) rate in the IMPC group", "number_stated": true, "source_locator": "chars 1378-1500 of source sha256 670d0f3c400a9ec12fb132f47497827e1c8a2a6491abae3fa5b9d9322491647c"}, "recorded_at": "2026-10-31T15:31:05.792505+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "fd793bc56b78cbe3ff005ab23894642ed569ee6c1021702c12b75200940cf22a", "source_hash": "670d0f3c400a9ec12fb132f47497827e1c8a2a6491abae3fa5b9d9322491647c", "raw_response": "<think>We need answer JSON only. Need identify single numerical result headline for registered target main finding. Paper main finding likely pCR rate IMPC vs non-IMPC overall: 21.6% vs 47.1%. Asked \"single numerical result\" and report headline number only: value paper itself states for registered target, not calculated. Registered target vague \"headline numerical result paper states for its main finding.\" Need choose parent_value likely 21.6, unit %. Evidence exact contiguous quote containing number, whole clause attribution. Could perhaps headline result is pCR rates 21.6% vs 47.1%. But schema singular parent_value. \"single numerical result that a replication ... has to reproduce. Report headline number only\". The headline number attached to main target likely IMPC pCR overall =21.6%. Need evidence quote clause: \"The IMPC group exhibited significantly lower pCR rates compared to the non-IMPC group: 21.6% vs. 47.1% (P = 0.004) overall...\" This includes comparison, and target. But \"headline number only\" parent_value 21.6. Unit %.\n\nCould target perhaps 21.6% vs 47.1%; \"single numerical result\" could mean result statement includes pair? Yet schema parent_value numeric only, singular. Usually these tasks ask registered target likely a benchmark value from source, perhaps paper's headline numerical result. Need infer extraction conventions. They say attribution may be carried by parenthetical list, respectively, or direct words. Quote whole clause. Here direct wording identifies \"IMPC group\" and lower pCR compared to non, then values respectively by order. Headline likely 21.6% for IMPC group. Evidence exact quote. target_result describe. JSON valid, no markdown.\n\nNeed ensure exact contiguous quotation and not shorten. Could quote: \"The IMPC group exhibited significantly lower pCR rates compared to the non-IMPC group: 21.6% vs. 47.1% (P = 0.004) overall, 15.0% vs. 28.4% (P = 0.223) in the H-based subgroup, and 27.8% vs. 57.6% (P = 0.017) in the HP-based subgroup.\" But whole clause enough, yet perhaps to establish \"overall\" include through \"(P = 0.004) overall\". Exact contiguous. Evidence contains both values and P; that's okay. Asked headline number only refers output fields likely no extra numerical values in target_result. But evidence necessarily contains numbers plural. Could quote minimal contiguous clause: \"The IMPC group exhibited significantly lower pCR rates compared to the non-IMPC group: 21.6% vs. 47.1% (P = 0.004) overall\" Is that a grammatical exact contiguous quotation? Yes from source before comma. No ellipsis. Attribution clear. Parent_value 21.6. unit \"%\". target_result maybe \"Overall pathological complete response rate in the IMPC group.\" Avoid numerical mention. number_stated true.\n\nQuestion: \"find the single numerical result that a replication of the registered target has to reproduce.\" Could headline numerical result perhaps 244 patients? Main finding headline is lower pCR, likely 21.6%. Need choose. Let's scrutinize title/abstract. Abstract reports n 244, subgroup counts, pCR 21.6 vs 47.1 overall and subgroups, survival P values, CTNNB1. Which is \"headline numerical result\"? Usually benchmark questions might target a specific number like \"pCR in IMPC group.\" They registered target generic, no named endpoint, says headline numerical result paper states for its main finding. Main claim resistance, numerical centerpiece pCR rate 21.6%. So yes.\n\nCould parent_value perhaps 47.1? Headline \"IMPC lower pCR compared to non-IMPC: 21.6% vs 47.1%\" and target main finding may be difference? No difference not stated, cannot calculate. User explicitly no calculated. The first number 21.6 is headline for IMPC main finding. Unit printed \"%\". Evidence should maybe include full sentence as exact contiguous quotation to show attribution. They warn \"When that is how the text links them, quote the whole clause so a reader can check the attribution for themselves.\" Entire clause sentence perhaps. Use entire sentence including subgroup rates. But \"Report headline number only\" perhaps evidence can contain all, since quote exact and no shortening. They explicitly evidence exact contiguous quote containing number; do not shorten it. \"do not shorten it\" means likely quote source passage, perhaps whole clause. Let's quote sentence exactly. parent_value only headline number. target_result no other number.\n\nJSON string escaping. Ensure unicode okay. Could use β irrelevant.\n\nLet's formulate:\n{\n \"parent_value\":21.6,\n \"unit\":\"%\",\n \"evidence\":\"The IMPC group exhibited significantly lower pCR rates compared to the non-IMPC group: 21.6% vs. 47.1% (P = 0.004) overall, 15.0% vs. 28.4% (P = 0.223) in the H-based subgroup, and 27.8% vs. 57.6% (P = 0.017) in the HP-based subgroup.\",\n \"target_result\":\"Overall pathological complete response (pCR) rate in the IMPC group.\",\n \"number_stated\":true\n}\n\nDoes evidence include multiple numbers but okay. Could quote only clause up to overall, but \"do not shorten it\" suggests full sentence. Good.\n\nNeed reply JSON object only, no code fence.</think>\n\n{\"parent_value\":21.6,\"unit\":\"%\",\"evidence\":\"The IMPC group exhibited significantly lower pCR rates compared to the non-IMPC group: 21.6% vs. 47.1% (P = 0.004) overall, 15.0% vs. 28.4% (P = 0.223) in the H-based subgroup, and 27.8% vs. 57.6% (P = 0.017) in the HP-based subgroup.\",\"target_result\":\"Overall pathological complete response (pCR) rate in the IMPC group.\",\"number_stated\":true}", "reading": {"parent_value": 21.6, "unit": "%", "evidence": "The IMPC group exhibited significantly lower pCR rates compared to the non-IMPC group: 21.6% vs. 47.1% (P = 0.004) overall, 15.0% vs. 28.4% (P = 0.223) in the H-based subgroup, and 27.8% vs. 57.6% (P = 0.017) in the HP-based subgroup.", "target_result": "Overall pathological complete response (pCR) rate in the IMPC group.", "number_stated": true, "source_locator": "chars 1378-1612 of source sha256 670d0f3c400a9ec12fb132f47497827e1c8a2a6491abae3fa5b9d9322491647c"}, "recorded_at": "2026-10-31T15:31:07.823079+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "The IMPC group had a lower overall pathological complete response rate than the non-IMPC group: 21.6% versus 47.1% (P = 0.004).", "minimax_alt": "The IMPC group exhibited significantly lower pCR rates compared to the non-IMPC group: 21.6% vs. 47.1% (P = 0.004) overall, 15.0% vs. 28.4% (P = 0.223) in the H-based subgroup, and 27.8% vs. 57.6% (P = 0.017) in the HP-based subgroup.", "decisive": false}, "physical_methods": {"minimax": ["To validate bioinformatics findings, matched pretreatment tumor samples from both groups were analyzed."], "minimax_alt": ["Validation using matched pretreatment tumor samples from both groups", "Assessment of tumor-infiltrating lymphocytes, CD4+ and CD8+ T cells, M2 macrophages, and PD-L1 expression in matched tumor samples"], "decisive": false}, "analysis_methods": {"minimax": ["Differentially expressed genes (DEGs) were identified using the “limma” R package with criteria of adjusted P-value < 0.05 and |logFC| ≥ 1.", "Enrichment analysis for Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) was performed using “ClusterProfiler” with a significance threshold of corrected P-value < 0.05.", "The protein-protein interaction (PPI) network for Homo sapiens was built using the STRING database with a minimum confidence score of 0.4.", "Hub genes were identified using the CytoHubba plugin with the maximal clique centrality (MCC) algorithm.", "Immune cell abundance was assessed by ImmuCellAI."], "minimax_alt": ["Retrospective IMPC versus non-IMPC comparison of baseline clinical and pathological characteristics, pCR rates, and survival outcomes", "R v4.0.4 normalization of the GSE66418 gene-expression matrix", "Differential expression analysis using the “limma” R package with adjusted P-value < 0.05 and |logFC| ≥ 1", "KEGG and Gene Ontology enrichment analysis using “ClusterProfiler” with corrected P-value < 0.05", "STRING protein-protein interaction network construction", "Cytoscape and CytoHubba hub-gene identification using the maximal clique centrality algorithm", "Immune-cell abundance assessment using ImmuCellAI"], "decisive": false}}, "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": "passed", "reason": "The independent readings are incomplete or disagree; 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