Iter-4360dd15-0103-transcript
第 103 轮执行轨迹
→ call search_memory({"limit":8,"query":"4360dd15 38310895 Europe PMC references PMID 原始试验"})【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0097-transcript", "tags": "iteration transcript", "modified": "20260424211821000", "preview": "!! 第 97 轮执行轨迹
→ call search_memory({\"limit\":8,\"query\":\"4360dd15 38310895 参考文献 原始人类试验 PMID mTOR rapalog 主要终点\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0060-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424200117000\", \"preview\": \"!! 第 60 轮执行轨迹 → call search_memory({\"limit\":8,\"query\":\"4360dd15 38310895 Europe PMC references human trial PMID\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0097-transcript\", \"tags\": \"i → call list_recent({"n":6})
→ call list_by_tag({"limit":20,"tag":"4360dd15"})
→ call list_tools({})
【tool:list_recent】
{"ok": true, "items": [{"title": "Iter-4360dd15-0102-reflection", "modified": "20260424213132000", "tags": "iteration reflection"}, {"title": "NEXT_FOCUS", "modified": "20260424213132000", "tags": "pinned focus"}, {"title": "先验明响应格式再写解析器", "modified": "20260424213132000", "tags": "lesson evidence-chain parsing europ-pmc"}, {"title": "Iter-4360dd15-0102-transcript", "modified": "20260424213124000", "tags": "iteration transcript"}, {"title": "Iter-4360dd15-0101-reflection", "modified": "20260424212846000", "tags": "iteration reflection"}, {"title": "先拿全量参考文献再分类", "modified": "20260424212846000", "tags": "lesson evidence-chain clinical-trials pmid"}]}
【tool:list_by_tag】
{"ok": true, "items": [{"title": "Iter-4360dd15-0100-human-trial-vs-non-original-screening-of-38310895-references", "modified": "20260424212530000"}, {"title": "Iter-4360dd15-0099-critic-mechanistic-vs-aging-trial", "modified": "20260424212312000"}, {"title": "Iter-4360dd15-0098-EuropePMC-extract-human-trial-PMIDs", "modified": "20260424212055000"}, {"title": "PMID 22367193 is cardiac-repolarization safety, not longevity evidence", "modified": "20260424210833000"}, {"title": "PMID 24691032 is muscle-protein-synthesis endpoint, not longevity evidence", "modified": "20260424210355000"}, {"title": "PMID 22115710 is phase I ocular safety study, not longevity evidence", "modified": "20260424210145000"}, {"title": "PMID 29408453 is feasibility/safety pilot, not direct longevity evidence", "modified": "20260424210012000"}, {"title": "PMID 31761958 is skin-senescence endpoint, not longevity evidence", "modified": "20260424205759000"}, {"title": "PMID 33977284 is RTI incidence endpoint, not direct longevity evidence", "modified": "20260424204839000"}, {"title": "PMID 25540326 is immune-response endpoint, not longevity evidence", "modified": "20260424204718000"}, {"title": "PMID 27883166 is a pilot safety feasibility trial not direct longevity evidence", "modified": "20260424204543000"}, {"title": "PEARL trial is not direct longevity evidence", "modified": "20260424203525000"}, {"title": "Iter-4360dd15-0078-two-pmid-evidence-verification", "modified": "20260424203242000"}, {"title": "I
【tool:list_tools】
{"ok": true, "tools": [{"name": "search_memory", "description": "在 TiddlyWiki 长期记忆中按关键字搜索（支持中文空格分隔），返回标题、标签、预览。每轮迭代开始前应先调用以回忆。", "custom": false}, {"name": "read_note", "description": "读取某一条 tiddler 的完整正文。", "custom": false}, {"name": "write_note", "description": "向 TiddlyWiki 写入（或覆盖）一条 tiddler。这是 Sisyphus 的长期记忆入口——每轮至少写一条。建议标签：knowledge, experiment, reflection, plan, idea, fact, question, lesson。TiddlyWiki 标记：!! 小标题，''粗体''，//斜体//，[[其它tiddler]]。", "custom": false}, {"name": "list_recent", "description": "列出最近修改过的 tiddler。", "custom": false}, {"name": "list_by_tag", "description": "按标签列出相关 tiddler。", "custom": false}, {"name": "run_python", "description": "在 workspace/ 下以子进程执行一段 Python 代码，返回 stdout/stderr。用于计算、模拟、验证假设、抓取公开数据（禁止任何破坏性操作）。", "custom": false}, {"name": "read_file", "description": "读取 workspace/ 下的某个文件。", "custom": false}, {"name": "write_file", "description": "向 workspace/ 下写入文件（默认覆盖，append=true 时追加）。", "custom": false}, {"name": "list_files", "description": "列出 workspace/ 下的文件。", "custom": false}, {"name": "web_fetch", "description": "抓取任意公开 URL（GET），返回剥离 HTML 后的纯文本。适合读论文摘要、文档、博客、百科。", "custom": false}, {"name": "web_search", "description": "用 DuckDuckGo 搜索互联网，返回 title/url/snippet 列表。找入口、找链接、调研时用。", "custom": false}, {"name": "wiki_search", "description": "维基百科搜索：返回若干条目的摘要和 URL。lang 默认 en，可传 zh 等。", "custom": false}, {"name": "arxiv_search", "description": "arXiv 论文检索：标题/作者/摘要/链接。理论、数学、物理、CS、bio 类前沿论文的主入口。", "custom": false}, {"name": "pubmed_search", "descriptio
→ call read_note({"title":"NEXT_FOCUS"})
→ call read_note({"title":"Iter-4360dd15-0102-reflection"})
→ call read_note({"title":"Iter-4360dd15-0100-human-trial-vs-non-original-screening-of-38310895-references"})
【tool:read_note】
{"ok": true, "title": "NEXT_FOCUS", "tags": "pinned focus", "text": "!! 下轮焦点（来自 mission `4360dd15` · Iter-0102）\n\n最窄的下一步是把 PMID 38310895 的 Europe PMC 参考文献稳定解析成 PMID-标题列表，然后只对尚未复核的条目做“原始人体试验/非原始试验”判定。"}
【tool:read_note】
{"ok": true, "title": "Iter-4360dd15-0102-reflection", "tags": "iteration reflection", "text": "!! 本轮进展\n本轮已直接从 Europe PMC 拿到 PMID 38310895 的 75 条参考文献原文，并确认其中可继续筛选出人体原始试验候选 PMID。\n\n!! 失败 / 盲点\n把精力浪费在错误的自动化路径上：工具定义参数出错、Python 解析又因未先校准响应格式而空转，导致没有把参考文献真正结构化出来。\n\n!! 下轮焦点\n最窄的下一步是把 PMID 38310895 的 Europe PMC 参考文献稳定解析成 PMID-标题列表，然后只对尚未复核的条目做“原始人体试验/非原始试验”判定。\n"}
【tool:read_note】
{"ok": true, "title": "Iter-4360dd15-0100-human-trial-vs-non-original-screening-of-38310895-references", "tags": "4360dd15 knowledge fact method clinical-trials evidence-chain", "text": "!! PMID 38310895 参考文献的“原始人体试验 / 非原始试验”复核（第 100 轮）\n\n本轮只做一件事：把上一轮从 PMID 38310895 的 Europe PMC 参考文献里抽出来的一批候选 PMID，用 PubMed 逐条复核为“原始人体试验 / 非原始试验”。\n\n!! 复核方法\n# 先以前轮抽取的候选 PMID 为种子。\n# 再用 PubMed 逐条确认题名、期刊与研究设计词。\n# 判据：题名明确出现 //follow-up//、//longitudinal analysis//、//extension//、//ancillary//、//postextension// 时，优先判为 //非原始试验//；其余 interventional / randomized / pilot / phase I/II/III 研究且为首次报告者，判为 //原始人体试验//。\n\n!! 本轮已复核的 PMID\n!! 原始人体试验（但不一定是长寿相关）\n* 33977284 — [[Targeting the biology of ageing with mTOR inhibitors to improve immune function in older adults: phase 2b and phase 3 randomised trials]]\n* 29408453 — [[A randomized control trial to establish the feasibility and safety of rapamycin treatment in an older human cohort: Immunological, physical performance, and cognitive effects]]\n* 32475067 — [[Dose-Dependent Acute Effects of Everolimus Administration on Immunological, Neuroendocrine and Psychological Parameters in Healthy Men]]\n* 35040506 — [[mTOR Inhibition with Sirolimus in Multiple System Atrophy: A Randomized, Double-Blind, Placebo-Controlled Futility Trial and 1-Year Biomarker Longitudinal Analysis]]\n* 25525171 — [[Intravitreal sirolimus for the treatment of geographic atrophy: results of a phase I/II clinical trial]]\n* 24618547 — [[Everolimus in patients with severe pulmonary hyp
→ call web_fetch({"max_chars":12000,"url":"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/references/1/1000"})
【tool:web_fetch】
{"ok": true, "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/references/1/1000", "status": 200, "content_type": "application/xml", "text": "6.9 75 38310895 MED 1 1000 33069325 MED JOURNAL ARTICLE Global age-sex-specific fertility, mortality, healthy life expectancy (HALE), and population estimates in 204 countries and territories, 1950-2019: a comprehensive demographic analysis for the Global Burden of Disease Study 2019. r Lancet 10258 2020 396 0140-6736 1474-547X 1160-1203 1 Y 28919117 MED JOURNAL ARTICLE Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. , Lancet 10100 2017 390 0140-6736 1474-547X 1211-1259 2 Y 37117804 MED JOURNAL ARTICLE The economic value of targeting aging. Scott AJ, Ellison M, Sinclair DA. Nat Aging 7 2021 1 2662-8465 2662-8465 616-623 3 Y 31316753 MED JOURNAL ARTICLE mTOR as a central regulator of lifespan and aging. Papadopoli D, Boulay K, Kazak L, Pollak M, Mallette FA, Topisirovic I, Hulea L. F1000Res 2019 8 2046-1402 2046-1402 F1000 Faculty Rev-998 4 Y 29190625 MED JOURNAL ARTICLE mTOR as Regulator of Lifespan, Aging, and Cellular Senescence: A Mini-Review. Weichhart T. Gerontology 2 2017 64 0304-324X 1423-0003 127-134 5 Y 36599349 MED JOURNAL ARTICLE Hallmarks of aging: An expanding universe. Lopez-Otin C, Blasco MA, Partridge L, Serrano M, Kroemer G. Cell 2 2023 1
→ call define_tool({"name":"parse_europepmc_references","description":"抓取并解析 Europe PMC 文献 references 接口，提取参考文献中的 PMID 与标题，返回结构化列表，便于后续筛选人体原始试验。","code":"import re\nimport requests\nimport xml.etree.ElementTree as ET\n\n\ndef run(**kwargs):\n source = kwargs.get('source')\n pmid = kwargs.get('pmid')\n if not source and not pmid:\n return {'ok': False, 'error': 'provide source url or pmid'}\n if no)
【tool:define_tool】
{"ok": false, "error": "参数错误: tool_define_tool() missing 1 required positional argument: 'parameters'"}
→ call run_python({"code":"import requests, re, xml.etree.ElementTree as ET, json\nurl='https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/references/1/1000'\nxml = requests.get(url, timeout=30).text\nprint('len', len(xml))\nprint(xml[:200])\n# Try parse as XML and inspect structure.\nroot = ET.fromstring(xml)\nprint('root', root.tag, root.attrib)\nprint('children', [c.tag for c in list(root)[:10]])\n# D)
【tool:run_python】
{"ok": true, "stdout": "len 42376\n<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?><responseWrapper xmlns:slx=\"http://www.scholix.org\" xmlns:epmc=\"https://www.europepmc.org/data\"><version>6.9</version><hitCount>75</hitCount><req\nroot responseWrapper {}\nchildren ['version', 'hitCount', 'request', 'referenceList']\nreference elements 75\n\nREF 1 tag reference attrib {}\ntext 33069325 MED JOURNAL ARTICLE Global age-sex-specific fertility, mortality, healthy life expectancy (HALE), and population estimates in 204 countries and territories, 1950-2019: a comprehensive demographic analysis for the Global Burden of Disease Study 2019. r Lancet 10258 2020 396 0140-6736 1474-547X 1160-1203 1 Y\n child id {} 33069325\n child source {} MED\n child citationType {} JOURNAL ARTICLE\n child title {} Global age-sex-specific fertility, mortality, healthy life expectancy (HALE), and population estimates in 204 countries \n child authorString {} r\n child journalAbbreviation {} Lancet\n child issue {} 10258\n child pubYear {} 2020\n child volume {} 396\n child ISSN {} 0140-6736\n\nREF 2 tag reference attrib {}\ntext 28919117 MED JOURNAL ARTICLE Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. , Lancet 10100 2017 390 0140-6736 1474-547X 1211-1259 2 Y\n child id {} 28919117\n child source {} MED\n child citationType {
→ call run_python({"code":"import requests, xml.etree.ElementTree as ET, re, json\nurl='https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/references/1/1000'\nxml = requests.get(url, timeout=30).text\nroot = ET.fromstring(xml)\nrefs = []\nfor ref in root.findall('.//reference'):\n pmid = (ref.findtext('id') or '').strip() or None\n title = (ref.findtext('title') or '').strip() or None\n auth = ()
【tool:run_python】
{"ok": true, "stdout": "total 75\n1 33069325 Global age-sex-specific fertility, mortality, healthy life expectancy (HALE), and populati\n2 28919117 Global, regional, and national incidence, prevalence, and years lived with disability for \n3 37117804 The economic value of targeting aging.\n21 19587680 Rapamycin fed late in life extends lifespan in genetically heterogeneous mice.\n41 18037627 Everolimus in patients with rheumatoid arthritis receiving concomitant methotrexate: a 3-m\n75 28579171 The NDR/LATS protein kinases in immunology and cancer biology.\nunreviewed likely original human trial candidates 4\nCAND 19963096 Intravenous temsirolimus in cancer patients: clinical pharmacology and dosing considerations.\nCAND 24151517 Systemic and nonrenal adverse effects occurring in renal transplant patients treated with mTOR inhibitors.\nCAND 30564495 Everolimus for treatment-refractory seizures in TSC: Extension of a randomized controlled trial.\nCAND 24267730 Safety and efficacy of everolimus with exemestane vs. exemestane alone in elderly patients with HER2-negative, hormone receptor-positive breast cancer in BOLERO-2.\nunreviewed others 51\nOTH 33069325 Global age-sex-specific fertility, mortality, healthy life expectancy (HALE), and population estimates in 204 countries and territories, 1950-2019: a comprehensive demographic analysis for the Global Burden of Disease Study 2019.\nOTH 28919117 Global, regional, and national incidence, prevalence, and years lived with disabili
→ call pubmed_search({"limit":5,"query":"30564495"})
→ call pubmed_search({"limit":5,"query":"24267730"})
→ call pubmed_search({"limit":5,"query":"19963096"})
【tool:pubmed_search】
{"ok": true, "query": "30564495", "results": [{"pmid": "30564495", "title": "Everolimus for treatment-refractory seizures in TSC: Extension of a randomized controlled trial.", "source": "Neurol Clin Pract", "pubdate": "2018 Oct", "authors": ["Franz DN", "Lawson JA", "Yapici Z", "Ikeda H", "Polster T", "Nabbout R", "Curatolo P", "de Vries PJ"], "url": "https://pubmed.ncbi.nlm.nih.gov/30564495/"}]}
【tool:pubmed_search】
{"ok": true, "query": "24267730", "results": [{"pmid": "24267730", "title": "Safety and efficacy of everolimus with exemestane vs. exemestane alone in elderly patients with HER2-negative, hormone receptor-positive breast cancer in BOLERO-2.", "source": "Clin Breast Cancer", "pubdate": "2013 Dec", "authors": ["Pritchard KI", "Burris HA 3rd", "Ito Y", "Rugo HS", "Dakhil S", "Hortobagyi GN", "Campone M", "Csöszi T"], "url": "https://pubmed.ncbi.nlm.nih.gov/24267730/"}]}
【tool:pubmed_search】
{"ok": true, "query": "19963096", "results": [{"pmid": "19963096", "title": "Intravenous temsirolimus in cancer patients: clinical pharmacology and dosing considerations.", "source": "Semin Oncol", "pubdate": "2009 Dec", "authors": ["Boni JP", "Hug B", "Leister C", "Sonnichsen D"], "url": "https://pubmed.ncbi.nlm.nih.gov/19963096/"}]}
→ call pubmed_search({"limit":5,"query":"24151517"})
【tool:pubmed_search】
{"ok": true, "query": "24151517", "results": [{"pmid": "24151517", "title": "Systemic and nonrenal adverse effects occurring in renal transplant patients treated with mTOR inhibitors.", "source": "Clin Dev Immunol", "pubdate": "2013", "authors": ["Zaza G", "Tomei P", "Ria P", "Granata S", "Boschiero L", "Lupo A"], "url": "https://pubmed.ncbi.nlm.nih.gov/24151517/"}]}
→ call write_note({"tags":["knowledge","fact","method","4360dd15","clinical-trials","evidence-chain"],"text":"!! PMID 38310895 的 Europe PMC 参考文献已稳定解析为 PMID-标题列表\n\n这轮把 `https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/references/1/1000` 解析成了结构化列表。\n\n!! 可复现解析方式\n* 返回格式是 XML，根节点为 `responseWrapper`，参考文献节点为 `reference`。\n* 每个 `reference` 里可直接读取：\n** `id` → PMID\n** `title` → 文献标题\n** `authorString` / `jou)
【tool:write_note】
{"ok": true, "path": "C:\\Users\\yh599\\Documents\\GitHub\\LLM-yh\\Sisyphus\\wiki\\tiddlers\\Iter-4360dd15-0103-EuropePMC-38310895-reference-parser-and-candidate-shortlist.tid", "title": "Iter-4360dd15-0103-EuropePMC-38310895-reference-parser-and-candidate-shortlist"}
【assistant】
本轮完成了一个最小但可复现的工程闭环：
- 已确认 Europe PMC 参考文献接口返回的是 **XML**
- 已稳定解析出 PMID 38310895 的 **75 条参考文献**
- 已把其中尚未复核的候选缩到 **4 条**
- 已用 PubMed 复核了其中 3 条的题名语义：
- **30564495**：`Extension of a randomized controlled trial`，应排除为“非首次原始报告”
- **24267730**：BOLERO-2 老年亚组安全/疗效分析，优先按“非新原始试验”处理
- **19963096**：更像临床药理/剂量讨论，不应直接算抗衰老原始试验
- **24151517**：转植后 mTOR 不良反应总结，也不该直接当作原始抗衰老试验
我还把这次的解析方式和候选短名单沉淀进了记忆。
<NEXT_FOCUS>下一轮只做一件事：逐条用 PubMed 给剩余 4 个候选 PMID 做“原始首次人体试验 / 非原始试验”最终判定，并把每条的排除理由写成可复用规则。</NEXT_FOCUS>