@synsci/cli-darwin-x64 1.1.70 → 1.1.72

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (339) hide show
  1. package/bin/skills/citation-management/SKILL.md +1109 -0
  2. package/bin/skills/citation-management/assets/bibtex_template.bib +264 -0
  3. package/bin/skills/citation-management/assets/citation_checklist.md +386 -0
  4. package/bin/skills/citation-management/references/bibtex_formatting.md +908 -0
  5. package/bin/skills/citation-management/references/citation_validation.md +794 -0
  6. package/bin/skills/citation-management/references/google_scholar_search.md +725 -0
  7. package/bin/skills/citation-management/references/metadata_extraction.md +870 -0
  8. package/bin/skills/citation-management/references/pubmed_search.md +839 -0
  9. package/bin/skills/citation-management/scripts/doi_to_bibtex.py +182 -0
  10. package/bin/skills/citation-management/scripts/extract_metadata.py +570 -0
  11. package/bin/skills/citation-management/scripts/format_bibtex.py +349 -0
  12. package/bin/skills/citation-management/scripts/search_google_scholar.py +251 -0
  13. package/bin/skills/citation-management/scripts/search_pubmed.py +348 -0
  14. package/bin/skills/citation-management/scripts/validate_citations.py +494 -0
  15. package/bin/skills/clinical-decision-support/README.md +129 -0
  16. package/bin/skills/clinical-decision-support/SKILL.md +506 -0
  17. package/bin/skills/clinical-decision-support/assets/biomarker_report_template.tex +380 -0
  18. package/bin/skills/clinical-decision-support/assets/clinical_pathway_template.tex +222 -0
  19. package/bin/skills/clinical-decision-support/assets/cohort_analysis_template.tex +359 -0
  20. package/bin/skills/clinical-decision-support/assets/color_schemes.tex +149 -0
  21. package/bin/skills/clinical-decision-support/assets/example_gbm_cohort.md +208 -0
  22. package/bin/skills/clinical-decision-support/assets/recommendation_strength_guide.md +328 -0
  23. package/bin/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +529 -0
  24. package/bin/skills/clinical-decision-support/references/biomarker_classification.md +719 -0
  25. package/bin/skills/clinical-decision-support/references/clinical_decision_algorithms.md +604 -0
  26. package/bin/skills/clinical-decision-support/references/evidence_synthesis.md +840 -0
  27. package/bin/skills/clinical-decision-support/references/outcome_analysis.md +640 -0
  28. package/bin/skills/clinical-decision-support/references/patient_cohort_analysis.md +427 -0
  29. package/bin/skills/clinical-decision-support/references/treatment_recommendations.md +521 -0
  30. package/bin/skills/clinical-decision-support/scripts/biomarker_classifier.py +383 -0
  31. package/bin/skills/clinical-decision-support/scripts/build_decision_tree.py +417 -0
  32. package/bin/skills/clinical-decision-support/scripts/create_cohort_tables.py +509 -0
  33. package/bin/skills/clinical-decision-support/scripts/generate_survival_analysis.py +441 -0
  34. package/bin/skills/clinical-decision-support/scripts/validate_cds_document.py +326 -0
  35. package/bin/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  36. package/bin/skills/clinical-reports/README.md +236 -0
  37. package/bin/skills/clinical-reports/SKILL.md +1127 -0
  38. package/bin/skills/clinical-reports/assets/case_report_template.md +352 -0
  39. package/bin/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  40. package/bin/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  41. package/bin/skills/clinical-reports/assets/consult_note_template.md +305 -0
  42. package/bin/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  43. package/bin/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  44. package/bin/skills/clinical-reports/assets/history_physical_template.md +305 -0
  45. package/bin/skills/clinical-reports/assets/lab_report_template.md +309 -0
  46. package/bin/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  47. package/bin/skills/clinical-reports/assets/quality_checklist.md +338 -0
  48. package/bin/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  49. package/bin/skills/clinical-reports/assets/soap_note_template.md +253 -0
  50. package/bin/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  51. package/bin/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  52. package/bin/skills/clinical-reports/references/data_presentation.md +530 -0
  53. package/bin/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  54. package/bin/skills/clinical-reports/references/medical_terminology.md +588 -0
  55. package/bin/skills/clinical-reports/references/patient_documentation.md +744 -0
  56. package/bin/skills/clinical-reports/references/peer_review_standards.md +585 -0
  57. package/bin/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  58. package/bin/skills/clinical-reports/scripts/check_deidentification.py +332 -0
  59. package/bin/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  60. package/bin/skills/clinical-reports/scripts/extract_clinical_data.py +97 -0
  61. package/bin/skills/clinical-reports/scripts/format_adverse_events.py +97 -0
  62. package/bin/skills/clinical-reports/scripts/generate_report_template.py +149 -0
  63. package/bin/skills/clinical-reports/scripts/terminology_validator.py +126 -0
  64. package/bin/skills/clinical-reports/scripts/validate_case_report.py +323 -0
  65. package/bin/skills/clinical-reports/scripts/validate_trial_report.py +88 -0
  66. package/bin/skills/fireworks-ai/SKILL.md +665 -0
  67. package/bin/skills/generate-image/SKILL.md +178 -0
  68. package/bin/skills/generate-image/scripts/generate_image.py +254 -0
  69. package/bin/skills/groq/SKILL.md +347 -0
  70. package/bin/skills/hypothesis-generation/SKILL.md +293 -0
  71. package/bin/skills/hypothesis-generation/assets/FORMATTING_GUIDE.md +672 -0
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  73. package/bin/skills/hypothesis-generation/assets/hypothesis_report_template.tex +572 -0
  74. package/bin/skills/hypothesis-generation/references/experimental_design_patterns.md +329 -0
  75. package/bin/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +198 -0
  76. package/bin/skills/hypothesis-generation/references/literature_search_strategies.md +622 -0
  77. package/bin/skills/latex-posters/README.md +417 -0
  78. package/bin/skills/latex-posters/SKILL.md +1602 -0
  79. package/bin/skills/latex-posters/assets/baposter_template.tex +257 -0
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  81. package/bin/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
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  83. package/bin/skills/latex-posters/references/latex_poster_packages.md +745 -0
  84. package/bin/skills/latex-posters/references/poster_content_guide.md +748 -0
  85. package/bin/skills/latex-posters/references/poster_design_principles.md +806 -0
  86. package/bin/skills/latex-posters/references/poster_layout_design.md +900 -0
  87. package/bin/skills/latex-posters/scripts/review_poster.sh +214 -0
  88. package/bin/skills/literature-review/SKILL.md +641 -0
  89. package/bin/skills/literature-review/assets/review_template.md +412 -0
  90. package/bin/skills/literature-review/references/citation_styles.md +166 -0
  91. package/bin/skills/literature-review/references/database_strategies.md +455 -0
  92. package/bin/skills/literature-review/scripts/generate_pdf.py +184 -0
  93. package/bin/skills/literature-review/scripts/search_databases.py +310 -0
  94. package/bin/skills/literature-review/scripts/verify_citations.py +218 -0
  95. package/bin/skills/market-research-reports/SKILL.md +904 -0
  96. package/bin/skills/market-research-reports/assets/FORMATTING_GUIDE.md +428 -0
  97. package/bin/skills/market-research-reports/assets/market_report_template.tex +1380 -0
  98. package/bin/skills/market-research-reports/assets/market_research.sty +564 -0
  99. package/bin/skills/market-research-reports/references/data_analysis_patterns.md +548 -0
  100. package/bin/skills/market-research-reports/references/report_structure_guide.md +999 -0
  101. package/bin/skills/market-research-reports/references/visual_generation_guide.md +1077 -0
  102. package/bin/skills/market-research-reports/scripts/generate_market_visuals.py +472 -0
  103. package/bin/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
  104. package/bin/skills/markitdown/LICENSE.txt +22 -0
  105. package/bin/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
  106. package/bin/skills/markitdown/QUICK_REFERENCE.md +309 -0
  107. package/bin/skills/markitdown/README.md +184 -0
  108. package/bin/skills/markitdown/SKILL.md +486 -0
  109. package/bin/skills/markitdown/SKILL_SUMMARY.md +307 -0
  110. package/bin/skills/markitdown/assets/example_usage.md +463 -0
  111. package/bin/skills/markitdown/references/api_reference.md +399 -0
  112. package/bin/skills/markitdown/references/file_formats.md +542 -0
  113. package/bin/skills/markitdown/scripts/batch_convert.py +195 -0
  114. package/bin/skills/markitdown/scripts/convert_literature.py +262 -0
  115. package/bin/skills/markitdown/scripts/convert_with_ai.py +224 -0
  116. package/bin/skills/ml-paper-writing/SKILL.md +937 -0
  117. package/bin/skills/ml-paper-writing/references/checklists.md +361 -0
  118. package/bin/skills/ml-paper-writing/references/citation-workflow.md +562 -0
  119. package/bin/skills/ml-paper-writing/references/reviewer-guidelines.md +367 -0
  120. package/bin/skills/ml-paper-writing/references/sources.md +159 -0
  121. package/bin/skills/ml-paper-writing/references/writing-guide.md +476 -0
  122. package/bin/skills/ml-paper-writing/templates/README.md +251 -0
  123. package/bin/skills/ml-paper-writing/templates/aaai2026/README.md +534 -0
  124. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026-unified-supp.tex +144 -0
  125. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026-unified-template.tex +952 -0
  126. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026.bib +111 -0
  127. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026.bst +1493 -0
  128. package/bin/skills/ml-paper-writing/templates/aaai2026/aaai2026.sty +315 -0
  129. package/bin/skills/ml-paper-writing/templates/acl/README.md +50 -0
  130. package/bin/skills/ml-paper-writing/templates/acl/acl.sty +312 -0
  131. package/bin/skills/ml-paper-writing/templates/acl/acl_latex.tex +377 -0
  132. package/bin/skills/ml-paper-writing/templates/acl/acl_lualatex.tex +101 -0
  133. package/bin/skills/ml-paper-writing/templates/acl/acl_natbib.bst +1940 -0
  134. package/bin/skills/ml-paper-writing/templates/acl/anthology.bib.txt +26 -0
  135. package/bin/skills/ml-paper-writing/templates/acl/custom.bib +70 -0
  136. package/bin/skills/ml-paper-writing/templates/acl/formatting.md +326 -0
  137. package/bin/skills/ml-paper-writing/templates/colm2025/README.md +3 -0
  138. package/bin/skills/ml-paper-writing/templates/colm2025/colm2025_conference.bib +11 -0
  139. package/bin/skills/ml-paper-writing/templates/colm2025/colm2025_conference.bst +1440 -0
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  142. package/bin/skills/ml-paper-writing/templates/colm2025/colm2025_conference.tex +305 -0
  143. package/bin/skills/ml-paper-writing/templates/colm2025/fancyhdr.sty +485 -0
  144. package/bin/skills/ml-paper-writing/templates/colm2025/math_commands.tex +508 -0
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  146. package/bin/skills/ml-paper-writing/templates/iclr2026/fancyhdr.sty +485 -0
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  167. package/bin/skills/paper-2-web/SKILL.md +491 -0
  168. package/bin/skills/paper-2-web/references/installation.md +141 -0
  169. package/bin/skills/paper-2-web/references/paper2poster.md +346 -0
  170. package/bin/skills/paper-2-web/references/paper2video.md +305 -0
  171. package/bin/skills/paper-2-web/references/paper2web.md +187 -0
  172. package/bin/skills/paper-2-web/references/usage_examples.md +436 -0
  173. package/bin/skills/peer-review/SKILL.md +702 -0
  174. package/bin/skills/peer-review/references/calibration_guidelines.md +196 -0
  175. package/bin/skills/peer-review/references/common_issues.md +552 -0
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  177. package/bin/skills/peer-review/references/reporting_standards.md +290 -0
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  179. package/bin/skills/pptx-posters/SKILL.md +410 -0
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  185. package/bin/skills/research-grants/README.md +285 -0
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  187. package/bin/skills/research-grants/assets/budget_justification_template.md +453 -0
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  191. package/bin/skills/research-grants/references/darpa_guidelines.md +636 -0
  192. package/bin/skills/research-grants/references/doe_guidelines.md +586 -0
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+ # Cell Press Writing Style Guide
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+
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+ Comprehensive writing guide for Cell, Neuron, Immunity, Molecular Cell, Developmental Cell, Cell Reports, and other Cell Press journals.
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+
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+ **Last Updated**: 2024
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+
7
+ ---
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+
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+ ## Overview
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+
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+ Cell Press journals emphasize **mechanistic depth**, **rigorous experimentation**, and **biological insight**. Unlike Nature/Science, which prioritize broad accessibility, Cell papers are written for biologists who appreciate technical detail and comprehensive data.
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+
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+ ### Key Philosophy
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+
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+ > "Cell papers tell a complete mechanistic story with exhaustive experimental support."
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+
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+ **Primary Goal**: Provide deep biological insight with extensive experimental validation that advances understanding of fundamental mechanisms.
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+
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+ ---
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+
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+ ## Unique Cell Press Features
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+
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+ Cell Press has several distinctive elements not found in other journals:
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+
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+ ### 1. Summary (Not Abstract)
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+
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+ Cell uses "Summary" instead of "Abstract" - functionally similar but emphasizes synthesis.
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+
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+ ### 2. Graphical Abstract (REQUIRED)
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+
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+ A visual summary appearing on the table of contents. **This is mandatory for all Cell Press journals.**
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+
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+ ### 3. eTOC Blurb
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+
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+ A 30-50 word "elevator pitch" for the electronic table of contents.
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+
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+ ### 4. Highlights
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+
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+ 3-4 bullet points (≤85 characters each) capturing key findings.
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+
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+ ### 5. In Brief
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+
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+ A one-sentence summary of the paper.
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+
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+ ---
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+
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+ ## Audience and Tone
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+
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+ ### Target Reader
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+
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+ - Expert biologist in the relevant field
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+ - Familiar with techniques and terminology
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+ - Expects comprehensive data and mechanistic depth
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+ - Values rigor and reproducibility
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+
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+ ### Tone Characteristics
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+
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+ | Characteristic | Description |
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+ |---------------|-------------|
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+ | **Technical** | Appropriate jargon for the field |
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+ | **Mechanistic** | Focus on how and why, not just what |
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+ | **Comprehensive** | Thorough exploration of the question |
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+ | **Data-rich** | Extensive experimental support |
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+ | **Precise** | Exact terminology and quantification |
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+
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+ ### Voice
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+
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+ - **First person ("we") acceptable**: "We demonstrate that..."
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+ - **Active voice encouraged**: "We identified..."
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+ - **Confident but measured**: Strong claims require strong evidence
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+
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+ ---
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+
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+ ## Summary (Abstract)
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+
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+ ### Style Requirements
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+
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+ - **150 words maximum** for Cell; varies for other Cell Press journals
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+ - **Flowing paragraph** (not structured sections)
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+ - **Dense with information**: Every sentence should convey key points
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+ - **Mechanistic focus**: What was discovered and how it works
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+
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+ ### Summary Structure
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+
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+ 1. **Context** (1 sentence): The biological question/problem
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+ 2. **Approach** (1 sentence): What you did
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+ 3. **Key findings** (2-4 sentences): Main results with mechanism
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+ 4. **Significance** (1 sentence): What this reveals about biology
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+
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+ ### Example Summary (Cell Style)
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+
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+ ```
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+ Cellular senescence is a stress response that arrests proliferation and
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+ promotes tissue remodeling, but the mechanisms controlling senescent cell
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+ fate remain unclear. Here, we identify the transcription factor FOXO4 as a
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+ critical regulator of senescent cell viability. FOXO4 is highly expressed
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+ in senescent cells and sequesters p53 away from mitochondria, preventing
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+ apoptosis. Using a cell-penetrating peptide that disrupts FOXO4-p53
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+ interaction, we selectively induce senescent cell apoptosis in vitro and
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+ in vivo. Administration of this peptide to aged mice restores fitness, fur
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+ density, and renal function. These findings reveal FOXO4-p53 as a senescence
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+ vulnerability and establish proof-of-concept for targeted senolytic
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+ interventions in aging.
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+ ```
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+
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+ ---
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+
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+ ## Graphical Abstract
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+
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+ ### Purpose
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+
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+ A single-panel visual summary for the table of contents that captures the entire paper's message.
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+
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+ ### Requirements
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+
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+ - **Size**: Square format, typically 1200 × 1200 pixels
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+ - **Layout**: Clean, uncluttered
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+ - **Content**: Show workflow, key finding, and mechanism
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+ - **Text**: Minimal labels, large readable fonts
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+ - **Color**: Vibrant but professional
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+
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+ ### Design Elements
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+
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+ ```
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+ Typical Graphical Abstract Components:
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+ 1. Starting point (cell, organism, condition)
127
+ 2. Intervention/treatment (arrows, symbols)
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+ 3. Key measurement or observation
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+ 4. Outcome/conclusion (visual representation)
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+ 5. Minimal text labels connecting elements
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+ ```
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+
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+ ### Example Description (for schematic generation)
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+
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+ ```
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+ "Graphical abstract showing: Left panel - normal cells with FOXO4 (blue)
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+ and p53 (green) separate. Center panel - senescent cells with FOXO4
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+ binding p53, preventing apoptosis. Right panel - FOXO4 peptide disrupts
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+ interaction, allowing p53 to reach mitochondria, triggering apoptosis.
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+ Arrow at bottom showing aged mouse → treatment → rejuvenated mouse."
141
+ ```
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+
143
+ ---
144
+
145
+ ## Highlights
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+
147
+ ### Format
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+
149
+ 3-4 bullet points, each ≤85 characters (including spaces)
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+
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+ ### Content Guidelines
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+
153
+ - Start with an action verb or key noun
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+ - Include specific findings
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+ - Make each highlight standalone
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+ - Cover different aspects of the paper
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+
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+ ### Example Highlights
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+
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+ ```
161
+ • FOXO4 is selectively expressed in senescent cells
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+
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+ • FOXO4 sequesters p53, preventing senescent cell apoptosis
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+
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+ • A FOXO4-targeting peptide induces selective senescent cell death
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+
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+ • Senolytic peptide treatment restores function in aged mice
168
+ ```
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+
170
+ ---
171
+
172
+ ## eTOC Blurb
173
+
174
+ ### Format
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+
176
+ 30-50 words for the electronic table of contents
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+
178
+ ### Writing Guidelines
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+
180
+ - Written by authors (editors may modify)
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+ - Start with author names or key finding
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+ - Make it a complete, engaging sentence
183
+ - Highlight the most exciting aspect
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+
185
+ ### Example eTOC Blurb
186
+
187
+ ```
188
+ Baar et al. identify FOXO4 as a vulnerability of senescent cells and
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+ develop a peptide that induces targeted apoptosis of senescent cells.
190
+ Treatment of aged mice with this senolytic peptide restores fitness
191
+ and organ function.
192
+ ```
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+
194
+ ---
195
+
196
+ ## Introduction
197
+
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+ ### Length and Structure
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+
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+ - **4-6 paragraphs** (800-1200 words)
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+ - More comprehensive than Nature/Science
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+ - Can include more technical detail and literature
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+
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+ ### Paragraph-by-Paragraph Guide
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+
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+ **Paragraph 1: Biological Context**
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+ - Establish the biological process or system
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+ - Why is this important to understand?
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+ - Set up the key players and mechanisms
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+
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+ **Paragraphs 2-3: State of the Field**
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+ - Detailed review of relevant prior work
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+ - Establish what is known mechanistically
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+ - More comprehensive than Nature/Science
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+
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+ **Paragraph 4: The Gap**
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+ - What remains unknown or controversial?
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+ - Why is this a critical question?
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+ - What has prevented progress?
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+
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+ **Paragraph 5: Your Approach**
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+ - How did you tackle this question?
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+ - What techniques/systems did you use?
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+ - Why was your approach appropriate?
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+
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+ **Final Paragraph: Key Findings Preview**
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+ - Brief statement of what you discovered
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+ - How does this advance the field?
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+ - Set up the structure of results
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+
231
+ ### Example Introduction Paragraph
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+
233
+ ```
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+ Cellular senescence is characterized by stable cell-cycle arrest, profound
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+ chromatin alterations, and a complex secretory phenotype known as the
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+ senescence-associated secretory phenotype (SASP) (Coppé et al., 2008;
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+ Rodier and Campisi, 2011). Senescent cells accumulate with age and at
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+ sites of pathology, where they can drive tissue dysfunction through
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+ SASP-mediated inflammation and disruption of tissue architecture (van
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+ Deursen, 2014). The targeted elimination of senescent cells—senolysis—has
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+ emerged as a promising therapeutic strategy, with genetic and pharmacological
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+ approaches demonstrating benefits in mouse models of aging and age-related
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+ disease (Baker et al., 2011, 2016; Chang et al., 2016).
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+ ```
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+
246
+ ---
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+
248
+ ## Results
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+
250
+ ### Organization
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+
252
+ Cell papers typically have **5-8 results sections**, each with a descriptive subheading:
253
+
254
+ ```
255
+ Results
256
+ ├── Section 1: Discovery of the phenomenon
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+ ├── Section 2: Characterization of the mechanism
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+ ├── Section 3: Identification of molecular players
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+ ├── Section 4: Functional validation
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+ ├── Section 5: In vivo confirmation
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+ ├── Section 6: Therapeutic proof-of-concept
262
+ └── Section 7: Broader implications
263
+ ```
264
+
265
+ ### Subheading Style
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+
267
+ Cell uses **declarative subheadings** stating the finding:
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+
269
+ ❌ "Analysis of FOXO4 expression" (descriptive - avoid)
270
+ ✅ "FOXO4 Is Selectively Upregulated in Senescent Cells" (declarative)
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+
272
+ ### Results Writing Style
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+
274
+ - **Comprehensive detail**: Cell expects more methodological context in Results than Nature
275
+ - **Figure-by-figure narrative**: Each major figure often corresponds to a results section
276
+ - **Statistical rigor**: All quantifications with statistics
277
+ - **Biological interpretation**: More interpretation woven in than pure Results sections
278
+
279
+ ### Example Results Paragraph
280
+
281
+ ```
282
+ To identify transcription factors regulating senescent cell viability, we
283
+ performed RNA sequencing on proliferating and senescent human fibroblasts
284
+ (IMR90 cells induced to senesce by replicative exhaustion, ionizing
285
+ radiation, or oncogene-induced senescence). Differential expression
286
+ analysis revealed 47 transcription factors significantly upregulated
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+ across all senescence modalities (FDR < 0.05, fold change > 2; Figure 1A
288
+ and Table S1). Among these, FOXO4 showed the highest and most consistent
289
+ upregulation (12.3 ± 2.1-fold; Figure 1B), a finding we confirmed by
290
+ quantitative RT-PCR (Figure 1C) and immunoblot analysis (Figure 1D).
291
+ Immunofluorescence microscopy revealed nuclear FOXO4 accumulation in
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+ senescent but not proliferating cells (Figure 1E,F).
293
+ ```
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+
295
+ ---
296
+
297
+ ## Discussion
298
+
299
+ ### Structure
300
+
301
+ Cell discussions are **thorough and mechanistic**:
302
+
303
+ **Paragraph 1: Summary**
304
+ - Restate key findings
305
+ - Synthesize the main message
306
+
307
+ **Paragraphs 2-4: Mechanistic Interpretation**
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+ - Deep dive into how your findings fit with known biology
309
+ - Propose models
310
+ - Discuss molecular mechanisms in detail
311
+
312
+ **Paragraph 5: Comparison with Literature**
313
+ - How do your findings relate to prior work?
314
+ - Resolve apparent contradictions
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+
316
+ **Paragraph 6: Implications and Applications**
317
+ - Therapeutic implications
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+ - Broader significance
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+
320
+ **Paragraph 7: Limitations**
321
+ - Honest assessment
322
+ - Open questions remaining
323
+
324
+ **Final Paragraph: Conclusions**
325
+ - Big-picture take-home message
326
+ - Future directions
327
+
328
+ ---
329
+
330
+ ## Experimental Procedures / STAR Methods
331
+
332
+ ### STAR Methods Format
333
+
334
+ Cell uses a structured **STAR Methods** section:
335
+
336
+ ```
337
+ RESOURCE AVAILABILITY
338
+ Lead Contact
339
+ Materials Availability
340
+ Data and Code Availability
341
+
342
+ EXPERIMENTAL MODEL AND SUBJECT DETAILS
343
+ Cell Lines
344
+ Animals
345
+ Human Subjects
346
+
347
+ METHOD DETAILS
348
+ [Detailed protocols for each technique]
349
+
350
+ QUANTIFICATION AND STATISTICAL ANALYSIS
351
+ ```
352
+
353
+ ### Key Reagent Table (KEY RESOURCES TABLE)
354
+
355
+ Cell requires a comprehensive table of all key resources:
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+
357
+ | REAGENT or RESOURCE | SOURCE | IDENTIFIER |
358
+ |---------------------|--------|------------|
359
+ | Antibodies | | |
360
+ | Rabbit anti-FOXO4 | Abcam | Cat#ab12345 |
361
+ | Chemicals | | |
362
+ | Doxorubicin | Sigma-Aldrich | Cat#D1515 |
363
+ | Cell Lines | | |
364
+ | IMR90 | ATCC | CCL-186 |
365
+
366
+ ---
367
+
368
+ ## Figures
369
+
370
+ ### Figure Philosophy
371
+
372
+ Cell papers are **figure-heavy** with extensive multi-panel figures:
373
+
374
+ - **6-8 main figures** typical
375
+ - **Multi-panel format**: 6-12 panels per figure common
376
+ - **Data-dense**: Comprehensive experimental support
377
+ - **Extended Data**: Supplementary figures for additional validation
378
+
379
+ ### Panel Labeling
380
+
381
+ Panels labeled with lowercase letters: **(A)**, **(B)**, **(C)**
382
+
383
+ ### Figure Legend Format
384
+
385
+ ```
386
+ Figure 3. FOXO4 Sequesters p53 in the Nucleus of Senescent Cells
387
+
388
+ (A) Immunofluorescence microscopy of p53 (green) and FOXO4 (red) in
389
+ proliferating (left) and senescent (right) IMR90 cells. DAPI (blue)
390
+ marks nuclei. Scale bar, 10 μm.
391
+
392
+ (B) Quantification of nuclear p53 intensity in proliferating versus
393
+ senescent cells. Data represent mean ± SEM; n = 3 biological replicates,
394
+ >100 cells per condition. ***p < 0.001, two-tailed Student's t test.
395
+
396
+ (C and D) Co-immunoprecipitation of FOXO4 and p53 in proliferating (C)
397
+ and senescent (D) cell lysates. IgG, immunoglobulin G control.
398
+
399
+ (E) Proximity ligation assay for FOXO4-p53 interaction. Red dots indicate
400
+ interaction events. Scale bar, 10 μm.
401
+
402
+ (F) Model of FOXO4-mediated p53 sequestration in senescent cells.
403
+
404
+ See also Figure S3 and Table S2.
405
+ ```
406
+
407
+ ---
408
+
409
+ ## References
410
+
411
+ ### Citation Style
412
+
413
+ - **Author-year format**: (Smith et al., 2023) or Smith et al. (2023)
414
+ - **Multiple citations**: (Smith et al., 2020; Jones et al., 2021)
415
+ - **Two authors**: (Smith and Jones, 2023)
416
+ - **Three or more**: (Smith et al., 2023)
417
+
418
+ ### Reference Format
419
+
420
+ ```
421
+ Baker, D.J., Wijshake, T., Tchkonia, T., LeBrasseur, N.K., Childs, B.G.,
422
+ van de Sluis, B., Kirkland, J.L., and van Deursen, J.M. (2011). Clearance
423
+ of p16Ink4a-positive senescent cells delays ageing-associated disorders.
424
+ Nature 479, 232–236.
425
+ ```
426
+
427
+ ---
428
+
429
+ ## Cell Press Journal Comparison
430
+
431
+ | Journal | Focus | Article Length | Figures |
432
+ |---------|-------|---------------|---------|
433
+ | **Cell** | Breakthrough biology | Long | 7-8 main + ED |
434
+ | **Neuron** | Neuroscience | Long | 6-8 main |
435
+ | **Immunity** | Immunology | Medium-Long | 6-7 main |
436
+ | **Molecular Cell** | Molecular mechanisms | Medium | 5-7 main |
437
+ | **Developmental Cell** | Development | Medium | 5-7 main |
438
+ | **Cell Reports** | Solid science | Medium | 4-6 main |
439
+
440
+ ---
441
+
442
+ ## Common Mistakes
443
+
444
+ 1. **Insufficient mechanism**: Describing what happens without how
445
+ 2. **Under-controlled experiments**: Missing key controls
446
+ 3. **Weak phenotype validation**: Single approach instead of multiple
447
+ 4. **Missing in vivo work**: Cell papers often expect animal studies
448
+ 5. **Incomplete figure panels**: Not showing all relevant conditions
449
+ 6. **Forgetting graphical abstract**: Required element
450
+ 7. **Exceeding highlight character limits**: ≤85 characters per bullet
451
+
452
+ ---
453
+
454
+ ## Pre-Submission Checklist
455
+
456
+ ### Required Elements
457
+ - [ ] Graphical abstract (square format)
458
+ - [ ] Highlights (3-4 bullets, ≤85 characters each)
459
+ - [ ] eTOC blurb (30-50 words)
460
+ - [ ] Summary (≤150 words)
461
+ - [ ] Key Resources Table
462
+
463
+ ### Content
464
+ - [ ] Mechanistic depth throughout
465
+ - [ ] Multiple complementary approaches
466
+ - [ ] In vivo validation (if applicable)
467
+ - [ ] Declarative subheadings
468
+ - [ ] Comprehensive figure panels
469
+
470
+ ### Style
471
+ - [ ] Technical precision in terminology
472
+ - [ ] Author-year citations
473
+ - [ ] Figure legends complete and standalone
474
+ - [ ] STAR Methods properly formatted
475
+
476
+ ---
477
+
478
+ ## See Also
479
+
480
+ - `venue_writing_styles.md` - Master style overview
481
+ - `journals_formatting.md` - Technical formatting requirements
482
+ - `nature_science_style.md` - Comparison with Nature/Science style
483
+