Iter-4360dd15-0038-transcript
第 38 轮执行轨迹
→ call search_memory({"limit":10,"query":"4360dd15 PMID 38310895 reference chain Crossref 75 references human trial rapamycin everolimus sirolimus"}) → call list_recent({"n":8})
→ call list_tools({})
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0037-transcript", "tags": "iteration transcript", "modified": "20260424191347000", "preview": "!! 第 37 轮执行轨迹
→ call search_memory({\"limit\":8,\"query\":\"4360dd15 rapamycin review 2024 trial endpoint remaining 11\"}) → call list_recent({\"n\":8}) → call list_by_tag({\"limit\":20,\"tag\":\"4360dd15\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0007-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424174944000\", \"preview\": \"!! 第 7 轮执行轨迹 → call search_memory({\"limit\":8,\"query\":\"4360dd15 rapamycin 2024 systematic review 19 studies Table 1 included trials endpoint\"}) → call list_recent({\"n\":6}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"tit【tool:list_recent】
{"ok": true, "items": [{"title": "Iter-4360dd15-0037-reflection", "modified": "20260424191353000", "tags": "iteration reflection"}, {"title": "NEXT_FOCUS", "modified": "20260424191353000", "tags": "pinned focus"}, {"title": "先拿引用数组再做精筛", "modified": "20260424191353000", "tags": "lesson evidence-retrieval crossref reference-chain"}, {"title": "Iter-4360dd15-0037-transcript", "modified": "20260424191347000", "tags": "iteration transcript"}, {"title": "Iter-4360dd15-0036-reflection", "modified": "20260424191122000", "tags": "iteration reflection"}, {"title": "先用 Crossref 参考数组替代网页正文", "modified": "20260424191122000", "tags": "lesson evidence-retrieval reference-chain crossref"}, {"title": "Iter-4360dd15-0036-transcript", "modified": "20260424191116000", "tags": "iteration transcript"}, {"title": "Error-20260425-030741", "modified": "20260424190741000", "tags": "error iteration"}]}
【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"})
【tool:read_note】
{"ok": true, "title": "NEXT_FOCUS", "tags": "pinned focus", "text": "!! 下轮焦点（来自 mission `4360dd15` · Iter-0037）\n\n把该综述 DOI 的 75 条 references 本地解析，并按 human trial / rapamycin / everolimus / sirolimus 精准过滤出剩余 11 项。"}
→ call search_memory({"limit":10,"query":"4360dd15 38310895 DOI Crossref references 75 human trial rapamycin everolimus sirolimus"})
→ call read_note({"title":"Iter-4360dd15-0037-reflection"})
→ call read_note({"title":"Iter-4360dd15-0036-reflection"})
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0037-transcript", "tags": "iteration transcript", "modified": "20260424191347000", "preview": "!! 第 37 轮执行轨迹
→ call search_memory({\"limit\":8,\"query\":\"4360dd15 rapamycin review 2024 trial endpoint remaining 11\"}) → call list_recent({\"n\":8}) → call list_by_tag({\"limit\":20,\"tag\":\"4360dd15\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0007-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424174944000\", \"preview\": \"!! 第 7 轮执行轨迹 → call search_memory({\"limit\":8,\"query\":\"4360dd15 rapamycin 2024 systematic review 19 studies Table 1 included trials endpoint\"}) → call list_recent({\"n\":6}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"tit【tool:read_note】
{"ok": true, "title": "Iter-4360dd15-0037-reflection", "tags": "iteration reflection", "text": "!! 本轮进展\n本轮确认了 PMID 38310895 的综述 DOI，并通过 Crossref 拿到了 75 条参考文献数组，打通了后续机器可读引用链入口。\n\n!! 失败 / 盲点\n本轮时间主要被 PubMed 403、Python 编码报错和工具语法错误消耗，未把参考文献继续筛成剩余 11 项人类研究。\n\n!! 下轮焦点\n把该综述 DOI 的 75 条 references 本地解析，并按 human trial / rapamycin / everolimus / sirolimus 精准过滤出剩余 11 项。\n"}
【tool:read_note】
{"ok": true, "title": "Iter-4360dd15-0036-reflection", "tags": "iteration reflection", "text": "!! 本轮进展\n已确认 PMID 38310895 对应综述并通过 Crossref 取到其 DOI 参考文献数组（75 条），为机器可读的引用链追踪打通了入口。\n\n!! 失败 / 盲点\n本轮主要耗在 PubMed 403、Python 编码报错和工具定义语法错误上，未把已拿到的参考列表继续过滤成“剩余 11 项人类研究”。\n\n!! 下轮焦点\n把该综述 DOI 的 75 条 references 本地解析并按“human trial / rapamycin / everolimus / sirolimus / 2024 review missing studies”精准过滤出剩余 11 项。\n"}
→ call search_memory({"limit":10,"query":"4360dd15 PMID 38310895 DOI review crossref"})
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0037-transcript", "tags": "iteration transcript", "modified": "20260424191347000", "preview": "!! 第 37 轮执行轨迹
→ call search_memory({\"limit\":8,\"query\":\"4360dd15 rapamycin review 2024 trial endpoint remaining 11\"}) → call list_recent({\"n\":8}) → call list_by_tag({\"limit\":20,\"tag\":\"4360dd15\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0007-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424174944000\", \"preview\": \"!! 第 7 轮执行轨迹 → call search_memory({\"limit\":10,\"query\":\"4360dd15 38310895 Crossref reference rapamycin sirolimus everolimus mTOR\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0010-transcript\", \"ta → call search_memory({"limit":20,"query":"38310895 DOI PMID rapamycin review"})
→ call search_memory({"limit":20,"query":"38310895 crossref doi references"})
→ call search_memory({"limit":20,"query":"38310895 everolimus sirolimus review"})
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0037-transcript", "tags": "iteration transcript", "modified": "20260424191347000", "preview": "!! 第 37 轮执行轨迹
→ call search_memory({\"limit\":8,\"query\":\"4360dd15 rapamycin 2024 systematic review 19 studies Table 1 included trials endpoint\"}) → call list_recent({\"n\":6}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0010-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424175830000\", \"preview\": \"!! 第 10 轮执行轨迹 → call search_memory({\"limit\":8,\"query\":\"4360dd15 rapamycin review 2024 trial endpoint remaining 11\"}) → call list_recent({\"n\":8}) → call list_by_tag({\"limit\":20,\"tag\":\"4360dd15\"}) 【tool:search_memory】 {\"ok\【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0033-transcript", "tags": "iteration transcript", "modified": "20260424190229000", "preview": "!! 第 33 轮执行轨迹
→ call search_memory({\\\"limit\\\":8,\\\"query\\\":\\\"4360dd15 rapamycin review 2"}, {"title": "Iter-4360dd15-0036-transcript", "tags": "iteration transcript", "modified": "20260424191116000", "preview": "!! 第 36 轮执行轨迹 → "}, {"title": "Iter-4360dd15-0037-transcript", "tags": "iteration transcript", "modified": "20260424191347000", "preview": "!! 第 37 轮执行轨迹 【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0037-transcript", "tags": "iteration transcript", "modified": "20260424191347000", "preview": "!! 第 37 轮执行轨迹
→ call search_memory({\"limit\":8,\"query\":\"4360dd15 PMID 38310895 reference chain Crossref 75 references human trial rapamycin everolimus sirolimus\"}) → call list_recent({\"n\":8}) → call list_tools({}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0010-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424175830000\", \"preview\": \"!! 第 10"}, {"title": "Iter-4360dd15-0010-transcript", "tags": "iteration transcript", "modified": "20260424175830000", "preview": "!! 第 10 轮执行轨迹 → cal"}, {"title": "Iter-4360dd15-0011-transcript", "tags": "iteration transcript", "modified": "20260424180153000", "preview": "!! 第 11 轮执行轨迹 → call list_files({"subdir":""})
【tool:list_files】
{"ok": true, "files": []}
→ call web_search({"limit":8,"query":"PMID 38310895 rapamycin review DOI Crossref references"})
→ call pubmed_search({"limit":5,"query":"38310895"})
→ call web_search({"limit":8,"query":"38310895 rapamycin sirolimus everolimus review"})
【tool:web_search】
{"ok": true, "query": "PMID 38310895 rapamycin review DOI Crossref references", "results": [{"title": "Targeting ageing with rapamycin and its derivatives in humans: a ...", "url": "https://europepmc.org/article/MED/38310895", "snippet": "Rapamycin and its derivatives improved physiological parameters associated with ageing in the immune, cardiovascular, and integumentary systems of healthy individuals or individuals with ageing-related diseases."}, {"title": "Crossref Metadata Search", "url": "https://search.crossref.org/", "snippet": "Search the metadata of journal articles, books, standards, datasets & more"}, {"title": "PubMed", "url": "https://pubmed.ncbi.nlm.nih.gov/", "snippet": "PubMed® comprises more than 40 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites."}, {"title": "Rapamycin for longevity: the pros, the cons, and future perspectives", "url": "https://www.frontiersin.org/journals/aging/articles/10.3389/fragi.2025.1628187/full", "snippet": "A systematic review evaluated the effects of rapamycin and its derivatives on aging-related physiological changes and diseases and found improvements in the immune, cardiovascular, and integumentary systems but not in the endocrine, muscular, or neurological systems (Lee et al., 2024)."}, {"title": "Targeting ageing with rapamycin and its derivatives in humans: a ...", "url": "https://w
【tool:pubmed_search】
{"ok": true, "query": "38310895", "results": [{"pmid": "38310895", "title": "Targeting ageing with rapamycin and its derivatives in humans: a systematic review.", "source": "Lancet Healthy Longev", "pubdate": "2024 Feb", "authors": ["Lee DJW", "Hodzic Kuerec A", "Maier AB"], "url": "https://pubmed.ncbi.nlm.nih.gov/38310895/"}]}
【tool:web_search】
{"ok": true, "query": "38310895 rapamycin sirolimus everolimus review", "results": [{"title": "Rapamycin for longevity: the pros, the cons, and future perspectives", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12226543/", "snippet": "Importantly, we will discuss the gaps in knowledge, pitfalls, and potential for the use of rapamycin to prevent aging/age-related disease and discuss the lessons learned from achieving FDA approval of evirolimus for TSC-related seizures after many years of off-label use. Keywords: aging, sirolimus , epilepsy, everolimus , mTOR Introduction"}, {"title": "Targeting ageing with rapamycin and its derivatives in humans: a ...", "url": "https://www.thelancet.com/journals/lanhl/article/PIIS2666-7568(23)00258-1/fulltext", "snippet": "The protocol of this systematic review was registered with PROSPERO (CRD42022345827). We searched PubMed, Embase, SCOPUS, Cochrane, and Web of Science for full-text articles published from database inception to July 18, 2022. Key search terms included \" rapamycin \", \" sirolimus \", \" everolimus \", and \"temsirolimus\" (appendix pp 1-14)."}, {"title": "An overview of the efficacy and safety of everolimus in adult solid ...", "url": "https://www.sciencedirect.com/science/article/pii/S0955470X21000616", "snippet": "2. Pharmacokinetic properties of everolimus Everolimus was developed to improve the pharmacokinetic (PK) characteristics of its analog, rapamycin , also known as sirolimus [35, 36]. The introduction of a hy
→ call web_fetch({"max_chars":12000,"url":"https://www.thelancet.com/journals/lanhl/article/PIIS2666-7568(23)00258-1/fulltext"})
→ call web_fetch({"max_chars":12000,"url":"https://www.sciencedirect.com/science/article/pii/S2666756823002581"})
→ call web_fetch({"max_chars":8000,"url":"https://api.crossref.org/works/10.1016/S2666-7568(23)00258-1"})
【tool:web_fetch】
{"ok": false, "error": "Client error '403 Forbidden' for url 'https://www.thelancet.com/journals/lanhl/article/PIIS2666-7568(23)00258-1/fulltext'\nFor more information check: https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/403"}
【tool:web_fetch】
{"ok": false, "error": "Client error '403 Forbidden' for url 'https://www.sciencedirect.com/science/article/pii/S2666756823002581'\nFor more information check: https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/403"}
【tool:web_fetch】
{"ok": true, "url": "https://api.crossref.org/works/10.1016/S2666-7568(23)00258-1", "status": 200, "content_type": "application/json", "text": "{\"status\":\"ok\",\"message-type\":\"work\",\"message-version\":\"1.0.0\",\"message\":{\"indexed\":{\"date-parts\":2026,4,16,\"date-time\":\"2026-04-16T16:09:43Z\",\"timestamp\":1776355783729,\"version\":\"3.51.2\"},\"reference-count\":75,\"publisher\":\"Elsevier BV\",\"issue\":\"2\",\"license\":[{\"start\":{\"date-parts\":2024,2,1,\"date-time\":\"2024-02-01T00:00:00Z\",\"timestamp\":1706745600000},\"content-version\":\"tdm\",\"delay-in-days\":0,\"URL\":\"https:\\/\\/www.elsevier.com\\/tdm\\/userlicense\\/1.0\\/\"},{\"start\":{\"date-parts\":2024,2,1,\"date-time\":\"2024-02-01T00:00:00Z\",\"timestamp\":1706745600000},\"content-version\":\"tdm\",\"delay-in-days\":0,\"URL\":\"https:\\/\\/www.elsevier.com\\/legal\\/tdmrep-license\"},{\"start\":{\"date-parts\":2023,11,24,\"date-time\":\"2023-11-24T00:00:00Z\",\"timestamp\":1700784000000},\"content-version\":\"vor\",\"delay-in-days\":0,\"URL\":\"http:\\/\\/creativecommons.org\\/licenses\\/by\\/4.0\\/\"}],\"funder\":[{\"DOI\":\"10.13039\\/100020054\",\"name\":\"Lien Foundation\",\"doi-asserted-by\":\"publisher\",\"id\":[{\"id\":\"10.13039\\/100020054\",\"id-type\":\"DOI\",\"asserted-by\":\"publisher\"}]}],\"content-domain\":{\"domain\":[\"thelancet.com\",\"elsevier.com\",\"sciencedirect.com\"],\"crossmark-restriction\":true},\"short-container-title\":[\"The Lancet Healthy L
→ call run_python({"code":"import requests, re, json\nfrom collections import Counter\n\ndoi='10.1016/S2666-7568(23)00258-1'\nurl=f'https://api.crossref.org/works/{doi}'\nresp=requests.get(url, timeout=30, headers={'User-Agent':'Mozilla/5.0'})\nresp.raise_for_status()\nmsg=resp.json()['message']\nrefs=msg.get('reference',[])\nprint('ref_count', len(refs))\n# show keys distribution\nprint('keys_sample', sorted(set(k)
【tool:run_python】
{"ok": true, "stdout": "ndomised, double-blind, placebo-controlled study\njournal: Lancet\ndoi: 10.1016/S0140-6736(16)31419-2\nyear: 2016\nauthor: French\nunstructured: None\n\n### 40\ntitle: Everolimus for treatment-refractory seizures in TSC: extension of a randomized controlled trial\njournal: Neurol Clin Pract\ndoi: 10.1212/CPJ.0000000000000514\nyear: 2018\nauthor: Franz\nunstructured: None\ntrialish_count 20\n\n--trial 1 Targeting the biology of ageing with mTOR inhibitors to improve immune function in older adults: phase 2b and phase 3 randomised trials 10.1016/S2666-7568(21)00062-3 2021\n\n--trial 2 A single-dose placebo- and moxifloxacin-controlled study of the effects of temsirolimus on cardiac repolarization in healthy adults 10.1007/s00280-012-1845-7 2012\n\n--trial 3 Topical rapamycin reduces markers of senescence and aging in human skin: an exploratory, prospective, randomized trial 10.1007/s11357-019-00113-y 2019\n\n--trial 4 Rapamycin does not affect post-absorptive protein metabolism in human skeletal muscle 10.1016/j.metabol.2012.07.003 2013\n\n--trial 5 Rapamycin administration in humans blocks the contraction-induced increase in skeletal muscle protein synthesis 10.1113/jphysiol.2008.163816 2009\n\n--trial 6 Activation of mTORC1 signaling and protein synthesis in human muscle following blood flow restriction exercise is inhibited by rapamycin 10.1152/ajpendo.00600.2013 2014\n\n--trial 7 A randomized control trial to establish the feasibility and safety of r
→ call web_search({"limit":10,"query":"\"Targeting ageing with rapamycin and its derivatives in humans\" included studies table 1 pdf"})
【tool:web_search】
{"ok": true, "query": "\"Targeting ageing with rapamycin and its derivatives in humans\" included studies table 1 pdf", "results": [{"title": "Targeting ageing with rapamycin and its derivatives in humans: a ...", "url": "https://www.thelancet.com/journals/lanhl/article/PIIS2666-7568(23)00258-1/fulltext", "snippet": "Rapamycin and its derivatives (rapalogs) are inhibitors of mTOR, a major regulator of the ageing process. We aimed to summarise the effects of rapamycin and its derivatives on the severity of ageing-related physiological changes and disease in adults. A search across five databases yielded 18 400 unique articles, resulting in 19 included studies . Rapamycin and its derivatives improved ..."}, {"title": "Targeting ageing with rapamycin and its derivatives in humans: a ...", "url": "https://www.sciencedirect.com/science/article/pii/S2666756823002581", "snippet": "A search across five databases yielded 18 400 unique articles, resulting in 19 included studies . Rapamycin and its derivatives improved physiological parameters associated with ageing in the immune, cardiovascular, and integumentary systems of healthy individuals or individuals with ageing-related diseases."}, {"title": "PDF Targeting ageing with rapamycin and its derivatives in humans: a ...", "url": "https://www.thelancet.com/pdfs/journals/lanhl/PIIS2666-7568(23)00258-1.pdf", "snippet": "A search across five databases yielded 18 400 unique articles, resulting in 19 included studies . Rapamycin and its d
→ call web_fetch({"max_chars":12000,"url":"https://www.thelancet.com/pdfs/journals/lanhl/PIIS2666-7568(23)00258-1.pdf"})
【tool:web_fetch】
{"ok": false, "error": "Client error '403 Forbidden' for url 'https://www.thelancet.com/pdfs/journals/lanhl/PIIS2666-7568(23)00258-1.pdf'\nFor more information check: https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/403"}
→ call search_memory({"limit":20,"query":"4360dd15 remaining 11 studies names"})
→ call search_memory({"limit":20,"query":"4360dd15 included studies 19 names"})
→ call search_memory({"limit":20,"query":"4360dd15 trial list rapamycin everolimus sirolimus temsirolimus"})
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0037-transcrip
```