Iter-4360dd15-0098-transcript
第 98 轮执行轨迹
→ call search_memory({"limit":8,"query":"4360dd15 38310895 Europe PMC references human trial PMID rapamycin"}) → call list_recent({"n":8})
→ call list_by_tag({"limit":10,"tag":"lesson evidence-chain clinical-trials endpoint-classification"})
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0088-transcript", "tags": "iteration transcript", "modified": "20260424205606000", "preview": "!! 第 88 轮执行轨迹
→ call search_memory({\\\"limit\\\":10,\\\"query\\\":\\\"4360dd15 NEXT_FOCUS 剩余 10 条候选 PMID 研究类型 保留 排除 理"}, {"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 rapamycin 2024 systematic review 19 studies Table Europe PMC NEXT_FOCUS\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0010-tra【tool:list_recent】
{"ok": true, "items": [{"title": "Iter-4360dd15-0097-reflection", "modified": "20260424211826000", "tags": "iteration reflection"}, {"title": "NEXT_FOCUS", "modified": "20260424211826000", "tags": "pinned focus"}, {"title": "用可访问的镜像入口绕开 403", "modified": "20260424211826000", "tags": "lesson evidence-chain fulltext-access clinical-trials"}, {"title": "Iter-4360dd15-0097-transcript", "modified": "20260424211821000", "tags": "iteration transcript"}, {"title": "Iter-4360dd15-0096-reflection", "modified": "20260424211456000", "tags": "iteration reflection"}, {"title": "先拿到可访问的全文入口", "modified": "20260424211456000", "tags": "lesson evidence-chain fulltext-access clinical-trials"}, {"title": "Iter-4360dd15-0096-transcript", "modified": "20260424211452000", "tags": "iteration transcript"}, {"title": "Iter-4360dd15-0095-reflection", "modified": "20260424211152000", "tags": "iteration reflection"}]}
【tool:list_by_tag】
{"ok": true, "items": []}
→ 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-0097）\n\n下一轮只做一件事：通过 Europe PMC API 或可访问 PDF/补充材料提取 PMID 38310895 的纳入人体原始试验 PMID 列表。"}
→ call web_search({"limit":5,"query":"PMID 38310895 Europe PMC rapamycin systematic review reference list human trial PMID"})
→ call web_search({"limit":5,"query":"38310895 rapamycin systematic review Europe PMC references pdf"})
→ call web_search({"limit":5,"query":"site:europepmc.org 38310895 rapamycin review"})
【tool:web_search】
{"ok": true, "query": "PMID 38310895 Europe PMC rapamycin systematic review reference list human trial PMID", "results": [{"title": "Targeting ageing with rapamycin and its derivatives in ... - Europe PMC", "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. Overall, no significant effects on the endocrine, muscular, or neurological systems were found."}, {"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": "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 articles were organised and managed using Covidence systematic review software (Veritas Health Innovation, Melbourne, VIC, Australia). To establish the progress of rapamycin and its derivatives in ongoing human studies, we searched ClinicalTrials.gov for relevant trials from database inception to July 2, 2023."}, {"title": "Targeting ageing with rapamycin a... preview & related info - Mendeley", "url": "https://www.mende
【tool:web_search】
{"ok": true, "query": "38310895 rapamycin systematic review Europe PMC references pdf", "results": [{"title": "Targeting ageing with rapamycin and its derivatives in ... - Europe PMC", "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": "PMC Home", "url": "https://pmc.ncbi.nlm.nih.gov/", "snippet": "PMC is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM)."}, {"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": "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": "Targeting ageing with rapamycin and its derivatives in humans: a ...", "url": "https://www.researchgate.net/publication/377976071_Targeting_ageing_with_rapamycin_and_its_derivatives_in_humans_a_systematic_review", "snippet": "A recent systematic review of human studies sugges
【tool:web_search】
{"ok": true, "query": "site:europepmc.org 38310895 rapamycin review", "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. Overall, no significant effects on the endocrine, muscular, or neurological systems were found."}, {"title": "The effect of rapamycin and its analogues on age-related ...", "url": "https://europepmc.org/article/pmc/9637607", "snippet": "This systematic review aims to provide insights into the effect/s of rapamycin and rapalogues on the most prevalent age-related MSKD in human participants. Some studies measured multiple outcomes, so we focused on measurements/outcomes relevant to the review ."}, {"title": "The bioavailability of compounded and generic rapamycin in normative ...", "url": "https://europepmc.org/article/PPR/PPR896861", "snippet": "Finally, we contextualize our data with a brief review of the literature on the currently available knowledge of rapamycin's bioavailability in normative aging populations, and provide implications for the clinical use of rapamycin in longevity medicine moving forward."}, {"title": "The effect of rapamycin and its analogues on age-related ...", "url": "https://europepmc.org/article/MED/35861940", "
→ call web_fetch({"max_chars":12000,"url":"https://europepmc.org/article/MED/38310895"})
【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}
→ call web_search({"limit":8,"query":"Europe PMC REST MED 38310895 fullTextXML references"})
→ call web_search({"limit":8,"query":"Europe PMC API references PMID 38310895 full text xml"})
→ call web_search({"limit":8,"query":"europe pmc 38310895 api xml reference"})
【tool:web_search】
{"ok": false, "error": "[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1028)"}
【tool:web_search】
{"ok": true, "query": "Europe PMC API references PMID 38310895 full text xml", "results": [{"title": "API Reference | PyEuropePMC Documentation", "url": "https://jonasheinickebio.github.io/pyEuropePMC/api/", "snippet": "Data Models Article Represents a scientific article from Europe PMC . Attributes: title: Article title authors: List of author names journal: Journal name pub_year: Publication year pmid : PubMed ID pmcid: PMC ID doi: DOI abstract: Article abstract keywords: List of keywords mesh_terms: List of MeSH terms Citation Represents a citation to an article. Attributes: pmid : PubMed ID of citing article "}, {"title": "Europe PMC", "url": "https://europepmc.org/restfulwebservice", "snippet": "For background information on Europe PMC content refer to the Web Service Reference Guide (Sections 2 and 3) and What am I searching on Europe PMC ? The search module can be used to query search fields. Refer to the fields module, the search syntax reference or the Web Service Reference Guide for a list of available fields."}, {"title": "For Developers - PMC", "url": "https://pmc.ncbi.nlm.nih.gov/tools/developers/", "snippet": "Not all articles in PMC are available for text mining and other reuse. The PMC Cloud Service, PMC OAI-PMH Service, PMC FTP Service, E-Utilities and BioC API are the only services that may be used for automated retrieval of PMC content. Systematic retrieval (or bulk retrieval) of articles through any other automated process is prohibited."}, {"title": "tool
【tool:web_search】
{"ok": true, "query": "europe pmc 38310895 api xml reference", "results": [{"title": "Europe PMC", "url": "https://europepmc.org/restfulwebservice", "snippet": "For background information on Europe PMC content refer to the Web Service Reference Guide (Sections 2 and 3) and What am I searching on Europe PMC ? The search module can be used to query search fields. Refer to the fields module, the search syntax reference or the Web Service Reference Guide for a list of available fields."}, {"title": "API Reference | PyEuropePMC Documentation", "url": "https://jonasheinickebio.github.io/pyEuropePMC/api/", "snippet": "Robust Python toolkit for scientific literature analysis from Europe PMC"}, {"title": "For Developers - PMC", "url": "https://pmc.ncbi.nlm.nih.gov/tools/developers/", "snippet": "Not all articles in PMC are available for text mining and other reuse. The PMC Cloud Service, PMC OAI-PMH Service, PMC FTP Service, E-Utilities and BioC API are the only services that may be used for automated retrieval of PMC content. Systematic retrieval (or bulk retrieval) of articles through any other automated process is prohibited. License terms vary. Please refer to the license ..."}, {"title": "tooluniverse.europe_pmc_tool module - ToolUniverse Documentation", "url": "https://zitniklab.hms.harvard.edu/ToolUniverse/en/api/tooluniverse.europe_pmc_tool.html", "snippet": "API Keys and Authentication Tutorials Agentic Tools Tutorial Literature Search Tools Tutorial Clinical Guidelines Tools
→ call web_fetch({"max_chars":12000,"url":"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/references/1/1000"})
→ call web_fetch({"max_chars":12000,"url":"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/fullTextXML"})
→ call web_fetch({"max_chars":12000,"url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:38310895%20AND%20SRC:MED&format=json"})
【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
【tool:web_fetch】
{"ok": false, "error": "Client error '404 Not Found' for url 'https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/fullTextXML'\nFor more information check: https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/404"}
【tool:web_fetch】
{"ok": true, "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:38310895%20AND%20SRC:MED&format=json", "status": 200, "content_type": "application/json;charset=UTF-8", "text": "{\"version\":\"6.9\",\"hitCount\":1,\"request\":{\"queryString\":\"EXT_ID:38310895 AND SRC:MED\",\"internalQuery\":\"EXT_ID:38310895 AND SRC:MED\",\"resultType\":\"LITE\",\"cursorMark\":\"*\",\"pageSize\":25,\"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\"}]}}", "truncated": false}
→ call web_fetch({"max_chars":12000,"url":"https://www.thelancet.com/journals/lanhl/article/PIIS2666-7568(23)00258-1/fulltext"})
【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"}
→ call run_python({"code":"import requests, re\nurl='https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/references/1/1000?format=json'\nr=requests.get(url,timeout=30)\nprint(r.status_code)\nprint(r.text[:5000])","timeout":60})
→ call run_python({"code":"import requests\nurl='https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/references/1/1000'\nr=requests.get(url,timeout=30)\nprint(r.status_code)\nprint(r.text[:2000])","timeout":60})
【tool:run_python】
{"ok": true, "stdout": "200\n", "stderr": "Traceback (most recent call last):\n File \"C:\\Users\\yh599\\Documents\\GitHub\\LLM-yh\\Sisyphus\\workspace\\_run_1777065592482.py\", line 5, in <module>\n print(r.text[:5000])\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 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\nUnicodeEncodeError: 'charmap' codec can't encode character '\\u03b2' in position 4447: character maps to <undefined>\n", "returncode": 1}
【tool:run_python】
{"ok": true, "stdout": "200\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><request><id>38310895</id><source>MED</source><offSet>1</offSet><pageSize>1000</pageSize></request><referenceList><reference><id>33069325</id><source>MED</source><citationType>JOURNAL ARTICLE</citationType><title>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.</title><authorString>r</authorString><journalAbbreviation>Lancet</journalAbbreviation><issue>10258</issue><pubYear>2020</pubYear><volume>396</volume><ISSN>0140-6736</ISSN><ESSN>1474-547X</ESSN><pageInfo>1160-1203</pageInfo><citedOrder>1</citedOrder><match>Y</match></reference><reference><id>28919117</id><source>MED</source><citationType>JOURNAL ARTICLE</citationType><title>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.</title><authorString>,</authorString><journalAbbreviation>Lancet</journalAbbreviation><issue>10100</issue><pubYear>2017</pubYear><volume>390</volume><ISSN>0140-6736</ISSN><ESSN>1474-547X</ESSN><pageInfo>1211-1259</pageInfo><citedOrde
→ call run_python({"code":"import requests, re, xml.etree.ElementTree as ET\nxml = requests.get('https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/references/1/1000', timeout=30).text\n# Parse XML with namespaces\nroot = ET.fromstring(xml)\nrefs=[]\nfor ref in root.findall('.//reference'):\n pmid = ref.findtext('id')\n title = ref.findtext('title') or ''\n year = ref.findtext('pubYear') or ''\n)
【tool:run_python】
{"ok": true, "stdout": "h the feasibility and safety of rapamycin treatment in an older human cohort: Immunological, physical performance, and cognitive effects.\n22115710\t2011\tA randomized, dose-escalation study of subconjunctival and intravitreal injections of sirolimus in patients with diabetic macular edema.\n29806044\t2018\tTreatment of Geographic Atrophy with Intravitreal Sirolimus: The Age-Related Eye Disease Study 2 Ancillary Study.\n33593448\t2021\tIntravitreal sirolimus for persistent, exudative age-related macular degeneration: a Pilot Study.\n20847709\t2010\tA randomized pilot study of systemic immunosuppression in the treatment of age-related macular degeneration with choroidal neovascularization.\n35040506\t2022\tmTOR Inhibition with Sirolimus in Multiple System Atrophy: A Randomized, Double-Blind, Placebo-Controlled Futility Trial and 1-Year Biomarker Longitudinal Analysis.\n25525171\t2014\tIntravitreal sirolimus for the treatment of geographic atrophy: results of a phase I/II clinical trial.\n24618547\t2013\tEverolimus in patients with severe pulmonary hypertension: a safety and efficacy pilot trial.\n18037627\t2007\tEverolimus in patients with rheumatoid arthritis receiving concomitant methotrexate: a 3-month, double-blind, randomised, placebo-controlled, parallel-group, proof-of-concept study.\n31781682\t2019\tLow-Dose Sirolimus Immunoregulation Therapy in Patients with Active Rheumatoid Arthritis: A 24-Week Follow-Up of the Randomized, Open-Label, Paralle
→ call run_python({"code":"import requests, xml.etree.ElementTree as ET, re, json\nxml = requests.get('https://www.ebi.ac.uk/europepmc/webservices/rest/MED/38310895/references/1/1000', timeout=30).text\nroot=ET.fromstring(xml)\nrefs=[]\nfor ref in root.findall('.//reference'):\n pmid = ref.findtext('id')\n title = (ref.findtext('title') or '').strip()\n year = ref.findtext('pubYear') or ''\n refs.append)
【tool:run_python】
{"ok": true, "stdout": "284\t2021\tTargeting the biology of ageing with mTOR inhibitors to improve immune function in older adults: phase 2b and phase 3 randomised trials.\n22367193\t2012\tA single-dose placebo- and moxifloxacin-controlled study of the effects of temsirolimus on cardiac repolarization in healthy adults.\n31761958\t2019\tTopical rapamycin reduces markers of senescence and aging in human skin: an exploratory, prospective, randomized trial.\n22959478\t2012\tRapamycin does not affect post-absorptive protein metabolism in human skeletal muscle.\n19188252\t2009\tRapamycin administration in humans blocks the contraction-induced increase in skeletal muscle protein synthesis.\n24691032\t2014\tActivation of mTORC1 signaling and protein synthesis in human muscle following blood flow restriction exercise is inhibited by rapamycin.\n32475067\t2020\tDose-Dependent Acute Effects of Everolimus Administration on Immunological, Neuroendocrine and Psychological Parameters in Healthy Men.\n29408453\t2018\tA randomized control trial to establish the feasibility and safety of rapamycin treatment in an older human cohort: Immunological, physical performance, and cognitive effects.\n22115710\t2011\tA randomized, dose-escalation study of subconjunctival and intravitreal injections of sirolimus in patients with diabetic macular edema.\n33593448\t2021\tIntravitreal sirolimus for persistent, exudative age-related macular degeneration: a Pilot Study.\n20847709\t2010\tA randomized pilot s
→ call pubmed_search({"limit":5,"query":"\"Targeting the biology of ageing with mTOR inhibitors to improve immune function in older adults: phase 2b and phase 3 randomised trials\""})
→ call web_search({"limit":5,"query":"\"Targeting the biology of ageing with mTOR inhibitors to improve immune function in older adults: phase 2b and phase 3 randomised trials\" PMID"})
【tool:pubmed_search】
{"ok": true, "query": "\"Targeting the biology of ageing with mTOR inhibitors to improve immune function in older adults: phase 2b and phase 3 randomised trials\"", "results": [{"pmid": "33977284", "title": "Targeting the biology of ageing with mTOR inhibitors to improve immune function in older adults: phase 2b and phase 3 randomised trials.", "source": "Lancet Healthy Longev", "pubdate": "2021 May", "authors": ["Mannick JB", "Teo G", "Bernardo P", "Quinn D", "Russell K", "Klickstein L", "Marshall W", "Shergill S"], "url": "https://pubmed.ncbi.nlm.nih.gov/33977284/"}]}
【tool:web_search】
{"ok": true, "query": "\"Targeting the biology of ageing with mTOR inhibitors to improve immune function in older a