Iter-4360dd15-0033-transcript
第 33 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", "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 search_memory({\\\"limit\\"}, {"title": "Iter-4360dd15-0007-transcript", "tags": "iteration transcript", "modified": "20260424174944000", "preview": "!! 第 7 轮执行轨迹 → call read_note({"title":"NEXT_FOCUS"})
→ call list_recent({"n":5})
→ call list_tools({})
【tool:read_note】
{"ok": true, "title": "NEXT_FOCUS", "tags": "pinned focus", "text": "!! 下轮焦点（来自 mission 4360dd15 · Iter-0032）\n\n从 Crossref 的 reference 数组中抽取与 rapamycin/sirolimus/everolimus/mTOR 相关的条目，逐条定位那 11 项剩余纳入研究。"}
【tool:list_recent】
{"ok": true, "items": [{"title": "Iter-4360dd15-0032-reflection", "modified": "20260424190005000", "tags": "iteration reflection"}, {"title": "NEXT_FOCUS", "modified": "20260424190005000", "tags": "pinned focus"}, {"title": "先拿到可解析的参考文献源", "modified": "20260424190005000", "tags": "lesson evidence-retrieval reference-chain crossref"}, {"title": "Iter-4360dd15-0032-transcript", "modified": "20260424185959000", "tags": "iteration transcript"}, {"title": "Iter-4360dd15-0031-reflection", "modified": "20260424185749000", "tags": "iteration reflection"}]}
【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 web_search({"limit":5,"query":"PMID 38310895 rapamycin review crossref DOI reference list"})
→ call pubmed_search({"limit":5,"query":"38310895"})
→ call web_search({"limit":5,"query":"38310895 Crossref DOI title"})
→ call search_memory({"limit":8,"query":"4360dd15 38310895 title DOI"})
【tool:web_search】
{"ok": true, "query": "PMID 38310895 rapamycin review crossref DOI reference list", "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": "Targeting ageing with rapamycin and its derivatives in humans: a ...", "url": "https://nutrition-evidence.com/article/501551/targeting-ageing-with-rapamycin-and-its-derivatives-in-humans-a-systematic-review", "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."}, {"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
【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": false, "error": "[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1028)"}
【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\": 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 PMID 38310895 reference chain remaining 11 studies rapamycin review\"}) 【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 2024 systematic review 19 studies Table 1 included trials endpoint\"}) → call list_recent({\"n\":6}) 【tool:search_memory】 {\"ok\": true, \"results\": → call web_search({"limit":10,"query":"\"Targeting ageing with rapamycin and its derivatives in humans: a systematic review\" DOI"})
→ call web_fetch({"max_chars":6000,"url":"https://europepmc.org/article/MED/38310895"})
→ call web_fetch({"max_chars":6000,"url":"https://pubmed.ncbi.nlm.nih.gov/38310895/"})
【tool:web_search】
{"ok": true, "query": "\"Targeting ageing with rapamycin and its derivatives in humans: a systematic review\" DOI", "results": []}
【tool:web_fetch】
{"ok": true, "url": "https://europepmc.org/article/MED/38310895", "status": 200, "content_type": "text/html;charset=UTF-8", "text": "Europe PMC Europe PMC 1 Sign in | Create an account https://orcid.org https://plus.europepmc.org Europe PMC Menu About About Europe PMC Preprints in Europe PMC Funders Become a funder Governance Roadmap Outreach Tools Tools overview Article status monitor Grant finder External links service RSS feeds About SciLite annotations Annotations submission service Developers Developer resources Articles RESTful API Grants RESTful API API case studies SOAP web service Annotations API OAI service Bulk downloads Developers Forum Support User guide Search syntax guide Contact us Contact us Helpdesk Feedback Twitter Blog Tech blog Developer Forum Europe PMC plus NOTICE: The ORCID Claiming tool has been temporarily disabled, because of technical issues. Please check back in later.", "truncated": false}
【tool:web_fetch】
{"ok": false, "error": "Client error '403 Forbidden' for url 'https://pubmed.ncbi.nlm.nih.gov/38310895/'\nFor more information check: https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/403"}
→ call web_search({"limit":8,"query":"site:api.crossref.org \"Targeting ageing with rapamycin and its derivatives in humans: a systematic review\""})
→ call web_search({"limit":8,"query":"site:europepmc.org/api \"38310895\" DOI"})
→ call web_search({"limit":8,"query":"site:europepmc.org \"Targeting ageing with rapamycin and its derivatives in humans\" DOI"})
【tool:web_search】
{"ok": true, "query": "site:api.crossref.org \"Targeting ageing with rapamycin and its derivatives in humans: a systematic review\"", "results": []}
【tool:web_search】
{"ok": true, "query": "site:europepmc.org/api \"38310895\" DOI", "results": []}
【tool:web_search】
{"ok": true, "query": "site:europepmc.org \"Targeting ageing with rapamycin and its derivatives in humans\" DOI", "results": []}
→ call search_memory({"limit":10,"query":"4360dd15 crossref reference arrays PMID 38310895"})
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0010-transcript", "tags": "iteration transcript", "modified": "20260424175830000", "preview": "!! 第 10 轮执行轨迹
→ cal"}, {"title": "Iter-4360dd15-0032-transcript", "tags": "iteration transcript", "modified": "20260424185959000", "preview": "!! 第 32 轮执行轨迹 → call search_memory({\\\"limit\\\":8,\\\"query\\\":\\\"4360dd15 rapamycin revi"}, {"title": "Iter-4360dd15-0025-transcript", "tags": "iteration transcript", "modified": "20260424183856000", "preview": "!! 第 25 轮执行轨迹 → call run_python({"code":"import requests, json, re\npmid='38310895'\nurls=[\n f'https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:{pmid}%20SRC:MED&format=json&pageSize=1',\n f'https://www.ebi.ac.uk/europepmc/webservices/rest/{pmid}/fullTextXML',\n f'https://api.crossref.org/works?query.bibliographic={requests.utils.quote(\"Targeting ageing with rapamycin and its derivatives in humans: )
【tool:run_python】
{"ok": true, "stdout": "URL https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:38310895%20SRC:MED&format=json&pageSize=1\nstatus 200 ct application/json;charset=UTF-8\n{\"version\":\"6.9\",\"hitCount\":1,\"request\":{\"queryString\":\"EXT_ID:38310895 SRC:MED\",\"internalQuery\":\"EXT_ID:38310895 SRC:MED\",\"resultType\":\"LITE\",\"cursorMark\":\"*\",\"pageSize\":1,\"sort\":\"\",\"synonym\":false},\"resultList\":{\"result\":[{\"id\":\"38310895\",\"source\":\"MED\",\"pmid\":\"38310895\",\"doi\":\"10.1016/s2666-7568(23)00258-1\",\"title\":\"Targeting ageing with rapamycin and its derivatives in humans: a systematic review.\",\"authorString\":\"Lee DJW, Hodzic Kuerec A, Maier AB.\",\"journalTitle\":\"Lancet Healthy Longev\",\"issue\":\"2\",\"journalVolume\":\"5\",\"pubYear\":\"2024\",\"journalIssn\":\"2666-7568\",\"pageInfo\":\"e152-e162\",\"pubType\":\"research support, non-u.s. gov't; systematic review; journal article\",\"isOpenAccess\":\"N\",\"inEPMC\":\"N\",\"inPMC\":\"N\",\"hasPDF\":\"N\",\"hasBook\":\"N\",\"hasSuppl\":\"N\",\"citedByCount\":96,\"hasReferences\":\"Y\",\"hasTextMinedTerms\":\"Y\",\"hasDbCrossReferences\":\"N\",\"hasLabsLinks\":\"Y\",\"hasTMAccessionNumbers\":\"N\",\"firstIndexDate\":\"2024-02-05\",\"firstPublicationDate\":\"2024-02-01\"}]}}\nURL https://www.ebi.ac.uk/europepmc/webservices/rest/38310895/fullTextXML\nstatus 404 ct None\n\nURL https://api.crossref.org/works?query.bibliographic=Targeting%20ageing%20with%20rapamycin%20and%20its%
→ call define_tool({"name":"crossref_filter_references","description":"Fetch a Crossref work by DOI and filter its reference array by keyword(s) in the reference string/title/DOI. Useful for rapidly extracting relevant citations from a paper's bibliography.","code":"import json, re\nfrom urllib.parse import quote\nimport requests\n\ndef run(**kwargs):\n doi = kwargs.get('doi')\n keywords = kwargs.get('keywords)
【tool:define_tool】
{"ok": false, "error": "参数错误: tool_define_tool() missing 1 required positional argument: 'parameters'"}
→ call define_tool({"name":"crossref_filter_references","description":"Fetch a Crossref work by DOI and filter its reference array by keyword(s) in the reference string/title/DOI. Useful for rapidly extracting relevant citations from a paper's bibliography.","code":"import json, re\nfrom urllib.parse import quote\nimport requests\n\ndef run(**kwargs):\n doi = kwargs.get('doi')\n keywords = kwargs.get('keywords)
【tool:define_tool】
{"ok": false, "error": "参数错误: tool_define_tool() missing 1 required positional argument: 'parameters'"}
→ call define_tool({"parameters":{"name":"crossref_filter_references","description":"Fetch a Crossref work by DOI and filter its reference array by keyword(s) in the reference string/title/DOI. Useful for rapidly extracting relevant citations from a paper's bibliography.","code":"import json, re\nfrom urllib.parse import quote\nimport requests\n\ndef run(**kwargs):\n doi = kwargs.get('doi')\n keywords = kwargs)
【tool:define_tool】
{"ok": false, "error": "参数错误: tool_define_tool() missing 3 required positional arguments: 'name', 'description', and 'code'"}
→ call define_tool({"name":"crossref_filter_references","description":"Fetch a Crossref work by DOI and filter its reference array by keyword(s) in the reference string/title/DOI. Useful for rapidly extracting relevant citations from a paper's bibliography.","code":"import json, re\nfrom urllib.parse import quote\nimport requests\n\ndef run(**kwargs):\n doi = kwargs.get('doi')\n keywords = kwargs.get('keywords)
【tool:define_tool】
{"ok": false, "error": "参数错误: tool_define_tool() missing 1 required positional argument: 'parameters'"}
→ call define_tool({"name":"crossref_filter_references","description":"Fetch a Crossref work by DOI and filter its reference array by keyword(s) in the reference string/title/DOI. Useful for rapidly extracting relevant citations from a paper's bibliography.","code":"import json, re\nfrom urllib.parse import quote\nimport requests\n\ndef run(**kwargs):\n doi = kwargs.get('doi')\n keywords = kwargs.get('keywords)
【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, json, re\nfrom urllib.parse import quote\n\ndoi='10.1016/S2666-7568(23)00258-1'\nurl=f'https://api.crossref.org/works/{quote(doi)}'\nr=requests.get(url,timeout=30,headers={'User-Agent':'Mozilla/5.0'})\nr.raise_for_status()\nmsg=r.json()['message']\nrefs=msg.get('reference',[])\nkeywords=['rapamycin','sirolimus','everolimus','mTOR','rapalog']\n\ndef ref_blob(ref):\n par)
【tool:run_python】
{"ok": true, "stdout": "title: Targeting ageing with rapamycin and its derivatives in humans: a systematic review\nreference_count: 75\nmatched_count: 56\n\n# 4\n{\"idx\": 4, \"year\": \"2019\", \"author\": \"Papadopoli\", \"title\": \"mTOR as a central regulator of lifespan and aging\", \"doi\": \"10.12688/f1000research.17196.1\", \"blob\": \"mTOR as a central regulator of lifespan and aging | Papadopoli | F1000Res | 2019 | 998 | 8\"}\n\n# 5\n{\"idx\": 5, \"year\": \"2018\", \"author\": \"Weichhart\", \"title\": \"mTOR as regulator of lifespan, aging, and cellular senescence: a mini-review\", \"doi\": \"10.1159/000484629\", \"blob\": \"mTOR as regulator of lifespan, aging, and cellular senescence: a mini-review | Weichhart | Gerontology | 2018 | 127 | 64\"}\n\n# 7\n{\"idx\": 7, \"year\": \"2015\", \"author\": \"Weichhart\", \"title\": \"Regulation of innate immune cell function by mTOR\", \"doi\": \"10.1038/nri3901\", \"blob\": \"Regulation of innate immune cell function by mTOR | Weichhart | Nat Rev Immunol | 2015 | 599 | 15\"}\n\n# 9\n", "stderr": "Traceback (most recent call last):\n File \"C:\\Users\\yh599\\Documents\\GitHub\\LLM-yh\\Sisyphus\\workspace\\_run_1777057326082.py\", line 32, in <module>\n print(json.dumps(m, ensure_ascii=False))\n ~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"C:\\Python313\\Lib\\encodings\\cp1252.py\", line 19, in encode\n return codecs.charmap_encode(input,self.errors,encoding_table)[0]\n ~~~~~~~~~~~~~~~~~~~~~^^^^^^
→ call run_python({"code":"import requests, json, re, sys\nfrom urllib.parse import quote\nsys.stdout.reconfigure(encoding='utf-8')\ndoi='10.1016/S2666-7568(23)00258-1'\nmsg=requests.get(f'https://api.crossref.org/works/{quote(doi)}',timeout=30,headers={'User-Agent':'Mozilla/5.0'}).json()['message']\nrefs=msg.get('reference',[]) or []\nterms=['rapamycin','sirolimus','everolimus','mTOR','rapalog','mammalian target o)
【tool:run_python】
{"ok": true, "stdout": "le\": \"mTOR regulates memory CD8 T-cell differentiation\",\n \"doi\": \"10.1038/nature08155\",\n \"unstructured\": null\n },\n {\n \"idx\": 58,\n \"year\": \"2007\",\n \"author\": \"Gao\",\n \"title\": \"Contrasting effects of cyclosporine and rapamycin in de novo generation of alloantigen-specific regulatory T cells\",\n \"doi\": \"10.1111/j.1600-6143.2007.01842.x\",\n \"unstructured\": null\n },\n {\n \"idx\": 61,\n \"year\": \"2013\",\n \"author\": \"Yamanaka\",\n \"title\": \"Therapeutic potential and adverse events of everolimus for treatment of hepatocellular carcinoma—systematic review and meta-analysis\",\n \"doi\": \"10.1002/cam4.150\",\n \"unstructured\": null\n },\n {\n \"idx\": 62,\n \"year\": \"2013\",\n \"author\": \"Zaza\",\n \"title\": \"Systemic and nonrenal adverse effects occurring in renal transplant patients treated with mTOR inhibitors\",\n \"doi\": \"10.1155/2013/403280\",\n \"unstructured\": null\n },\n {\n \"idx\": 63,\n \"year\": \"2012\",\n \"author\": \"Woillard\",\n \"title\": \"Association of sirolimus adverse effects with m-TOR, p70S6K or raptor polymorphisms in kidney transplant recipients\",\n \"doi\": \"10.1097/FPC.0b013e328357359d\",\n \"unstructured\": null\n },\n {\n \"idx\": 64,\n \"year\": \"2014\",\n \"author\": \"Kaplan\",\n \"title\"
【assistant】
本轮结论：
1. **PMID 38310895 的准确书目信息已再次确认**
- 题名：*Targeting ageing with rapamycin and its derivatives in humans: a systematic review*
- DOI：**10.1016/S2666-7568(23)00258-1**
- 来源：Europe PMC / Crossref 元数据可直接拿到，且 **Crossref 返回的 reference 数组共 75 条**
2. **已成功从 Crossref reference 数组中抽出与目标相关的条目**
- 以 rapamycin / sirolimus / everolimus / mTOR / rapalog 为关键词过滤后，**命中 56 条**
- 这证明：这条参考文献链足够密，能继续从“文献列表层”向“纳入研究层”推进，而不必死磕 403 全文
3. **已经出现一批明显相关的“人类研究/临床研究”候选**
- Kaeberlein 2023 — *Evaluation of off-label rapamycin use to promote healthspan in 333 adults*，DOI **10.1007/s11357-023-00818-1**
- French 2016 — *EXIST-3* everolimus Ⅲ期试验，DOI **10.1016/S0140-6736(16)31419-2**
- Franz 2018 / 2021 — everolimus in TSC refractory seizures
- Tesch 2019 — 4EVER trial
- Pritchard 2013 — BOLERO-2 elderly subgroup
- 这些条目说明：**Crossref reference 链里确实包含了综述所纳入的临床试验线索**，下一步应做的是把它们和 Table 1 的“剩余 11 项”逐一对齐
4. **本轮最小可验证成果**
- 我已经把“继续盲搜全文”改成了“从 Crossref reference 数组里做定向筛选”
- 这是一个可复现的检索范式：PMID -> Crossref DOI -> reference[] -> keyword filter -> 候选临床研究
<NEXT_FOCUS>把 Crossref 命中的 56 条里，优先筛成“人类纳入研究”而不是基础机制文献，并逐条与综述 Table 1 的剩余 11 项做 DOI/题名对齐</NEXT_FOCUS>
```