@pikaa-ai/pikaa 0.3.1 → 0.3.5

package/skills/venue-templates/references/cell_press_style.md

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-# Cell Press Writing Style Guide
-
-Comprehensive writing guide for Cell, Neuron, Immunity, Molecular Cell, Developmental Cell, Cell Reports, and other Cell Press journals.
-
-**Reviewed**: 2026-07-20
-
-Cell Press requirements differ by journal and article type. Verify each front-matter and STAR Methods element in the current author instructions.
-
----
-
-## Overview
-
-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.
-
-### Key Philosophy
-
-> "Cell papers tell a complete mechanistic story with exhaustive experimental support."
-
-**Primary Goal**: Provide deep biological insight with extensive experimental validation that advances understanding of fundamental mechanisms.
-
----
-
-## Unique Cell Press Features
-
-Cell Press journals may use several distinctive elements not found in other journals:
-
-### 1. Summary (Not Abstract)
-
-Cell uses "Summary" instead of "Abstract" - functionally similar but emphasizes synthesis.
-
-### 2. Graphical Abstract
-
-A visual summary for discovery and the table of contents. It is required for some journals and article types; verify the current target-journal instructions.
-
-### 3. eTOC Blurb
-
-A 30-50 word "elevator pitch" for the electronic table of contents.
-
-### 4. Highlights
-
-3-4 bullet points (≤85 characters each) capturing key findings.
-
-### 5. In Brief
-
-A one-sentence summary of the paper.
-
----
-
-## Audience and Tone
-
-### Target Reader
-
-- Expert biologist in the relevant field
-- Familiar with techniques and terminology
-- Expects comprehensive data and mechanistic depth
-- Values rigor and reproducibility
-
-### Tone Characteristics
-
-| Characteristic | Description |
-|---------------|-------------|
-| **Technical** | Appropriate jargon for the field |
-| **Mechanistic** | Focus on how and why, not just what |
-| **Comprehensive** | Thorough exploration of the question |
-| **Data-rich** | Extensive experimental support |
-| **Precise** | Exact terminology and quantification |
-
-### Voice
-
-- **First person ("we") acceptable**: "We demonstrate that..."
-- **Active voice encouraged**: "We identified..." 
-- **Confident but measured**: Strong claims require strong evidence
-
----
-
-## Summary (Abstract)
-
-### Style Requirements
-
-- **150 words maximum** for Cell; varies for other Cell Press journals
-- **Flowing paragraph** (not structured sections)
-- **Dense with information**: Every sentence should convey key points
-- **Mechanistic focus**: What was discovered and how it works
-
-### Summary Structure
-
-1. **Context** (1 sentence): The biological question/problem
-2. **Approach** (1 sentence): What you did
-3. **Key findings** (2-4 sentences): Main results with mechanism
-4. **Significance** (1 sentence): What this reveals about biology
-
-### Example Summary (Cell Style)
-
-```
-Cellular senescence is a stress response that arrests proliferation and 
-promotes tissue remodeling, but the mechanisms controlling senescent cell 
-fate remain unclear. Here, we identify the transcription factor FOXO4 as a 
-critical regulator of senescent cell viability. FOXO4 is highly expressed 
-in senescent cells and sequesters p53 away from mitochondria, preventing 
-apoptosis. Using a cell-penetrating peptide that disrupts FOXO4-p53 
-interaction, we selectively induce senescent cell apoptosis in vitro and 
-in vivo. Administration of this peptide to aged mice restores fitness, fur 
-density, and renal function. These findings reveal FOXO4-p53 as a senescence 
-vulnerability and establish proof-of-concept for targeted senolytic 
-interventions in aging.
-```
-
----
-
-## Graphical Abstract
-
-### Purpose
-
-A single-panel visual summary for the table of contents that captures the entire paper's message.
-
-### Requirements
-
-- **Size**: Square format, typically 1200 × 1200 pixels
-- **Layout**: Clean, uncluttered
-- **Content**: Show workflow, key finding, and mechanism
-- **Text**: Minimal labels, large readable fonts
-- **Color**: Vibrant but professional
-
-### Design Elements
-
-```
-Typical Graphical Abstract Components:
-1. Starting point (cell, organism, condition)
-2. Intervention/treatment (arrows, symbols)
-3. Key measurement or observation
-4. Outcome/conclusion (visual representation)
-5. Minimal text labels connecting elements
-```
-
-### Example Description (for schematic generation)
-
-```
-"Graphical abstract showing: Left panel - normal cells with FOXO4 (blue) 
-and p53 (green) separate. Center panel - senescent cells with FOXO4 
-binding p53, preventing apoptosis. Right panel - FOXO4 peptide disrupts 
-interaction, allowing p53 to reach mitochondria, triggering apoptosis. 
-Arrow at bottom showing aged mouse → treatment → rejuvenated mouse."
-```
-
----
-
-## Highlights
-
-### Format
-
-3-4 bullet points, each ≤85 characters (including spaces)
-
-### Content Guidelines
-
-- Start with an action verb or key noun
-- Include specific findings
-- Make each highlight standalone
-- Cover different aspects of the paper
-
-### Example Highlights
-
-```
-• FOXO4 is selectively expressed in senescent cells
-
-• FOXO4 sequesters p53, preventing senescent cell apoptosis
-
-• A FOXO4-targeting peptide induces selective senescent cell death
-
-• Senolytic peptide treatment restores function in aged mice
-```
-
----
-
-## eTOC Blurb
-
-### Format
-
-30-50 words for the electronic table of contents
-
-### Writing Guidelines
-
-- Written by authors (editors may modify)
-- Start with author names or key finding
-- Make it a complete, engaging sentence
-- Highlight the most exciting aspect
-
-### Example eTOC Blurb
-
-```
-Baar et al. identify FOXO4 as a vulnerability of senescent cells and 
-develop a peptide that induces targeted apoptosis of senescent cells. 
-Treatment of aged mice with this senolytic peptide restores fitness 
-and organ function.
-```
-
----
-
-## Introduction
-
-### Length and Structure
-
-- **4-6 paragraphs** (800-1200 words)
-- More comprehensive than Nature/Science
-- Can include more technical detail and literature
-
-### Paragraph-by-Paragraph Guide
-
-**Paragraph 1: Biological Context**
-- Establish the biological process or system
-- Why is this important to understand?
-- Set up the key players and mechanisms
-
-**Paragraphs 2-3: State of the Field**
-- Detailed review of relevant prior work
-- Establish what is known mechanistically
-- More comprehensive than Nature/Science
-
-**Paragraph 4: The Gap**
-- What remains unknown or controversial?
-- Why is this a critical question?
-- What has prevented progress?
-
-**Paragraph 5: Your Approach**
-- How did you tackle this question?
-- What techniques/systems did you use?
-- Why was your approach appropriate?
-
-**Final Paragraph: Key Findings Preview**
-- Brief statement of what you discovered
-- How does this advance the field?
-- Set up the structure of results
-
-### Example Introduction Paragraph
-
-```
-Cellular senescence is characterized by stable cell-cycle arrest, profound 
-chromatin alterations, and a complex secretory phenotype known as the 
-senescence-associated secretory phenotype (SASP) (Coppé et al., 2008; 
-Rodier and Campisi, 2011). Senescent cells accumulate with age and at 
-sites of pathology, where they can drive tissue dysfunction through 
-SASP-mediated inflammation and disruption of tissue architecture (van 
-Deursen, 2014). The targeted elimination of senescent cells—senolysis—has 
-emerged as a promising therapeutic strategy, with genetic and pharmacological 
-approaches demonstrating benefits in mouse models of aging and age-related 
-disease (Baker et al., 2011, 2016; Chang et al., 2016).
-```
-
----
-
-## Results
-
-### Organization
-
-Cell papers typically have **5-8 results sections**, each with a descriptive subheading:
-
-```
-Results
-├── Section 1: Discovery of the phenomenon
-├── Section 2: Characterization of the mechanism  
-├── Section 3: Identification of molecular players
-├── Section 4: Functional validation
-├── Section 5: In vivo confirmation
-├── Section 6: Therapeutic proof-of-concept
-└── Section 7: Broader implications
-```
-
-### Subheading Style
-
-Cell uses **declarative subheadings** stating the finding:
-
-❌ "Analysis of FOXO4 expression" (descriptive - avoid)
-✅ "FOXO4 Is Selectively Upregulated in Senescent Cells" (declarative)
-
-### Results Writing Style
-
-- **Comprehensive detail**: Cell expects more methodological context in Results than Nature
-- **Figure-by-figure narrative**: Each major figure often corresponds to a results section
-- **Statistical rigor**: All quantifications with statistics
-- **Biological interpretation**: More interpretation woven in than pure Results sections
-
-### Example Results Paragraph
-
-```
-To identify transcription factors regulating senescent cell viability, we 
-performed RNA sequencing on proliferating and senescent human fibroblasts 
-(IMR90 cells induced to senesce by replicative exhaustion, ionizing 
-radiation, or oncogene-induced senescence). Differential expression 
-analysis revealed 47 transcription factors significantly upregulated 
-across all senescence modalities (FDR < 0.05, fold change > 2; Figure 1A 
-and Table S1). Among these, FOXO4 showed the highest and most consistent 
-upregulation (12.3 ± 2.1-fold; Figure 1B), a finding we confirmed by 
-quantitative RT-PCR (Figure 1C) and immunoblot analysis (Figure 1D). 
-Immunofluorescence microscopy revealed nuclear FOXO4 accumulation in 
-senescent but not proliferating cells (Figure 1E,F).
-```
-
----
-
-## Discussion
-
-### Structure
-
-Cell discussions are **thorough and mechanistic**:
-
-**Paragraph 1: Summary**
-- Restate key findings
-- Synthesize the main message
-
-**Paragraphs 2-4: Mechanistic Interpretation**
-- Deep dive into how your findings fit with known biology
-- Propose models
-- Discuss molecular mechanisms in detail
-
-**Paragraph 5: Comparison with Literature**
-- How do your findings relate to prior work?
-- Resolve apparent contradictions
-
-**Paragraph 6: Implications and Applications**
-- Therapeutic implications
-- Broader significance
-
-**Paragraph 7: Limitations**
-- Honest assessment
-- Open questions remaining
-
-**Final Paragraph: Conclusions**
-- Big-picture take-home message
-- Future directions
-
----
-
-## Experimental Procedures / STAR Methods
-
-### STAR Methods Format
-
-Cell uses a structured **STAR Methods** section:
-
-```
-RESOURCE AVAILABILITY
-  Lead Contact
-  Materials Availability
-  Data and Code Availability
-
-EXPERIMENTAL MODEL AND SUBJECT DETAILS
-  Cell Lines
-  Animals
-  Human Subjects
-
-METHOD DETAILS
-  [Detailed protocols for each technique]
-
-QUANTIFICATION AND STATISTICAL ANALYSIS
-```
-
-### Key Reagent Table (KEY RESOURCES TABLE)
-
-Cell requires a comprehensive table of all key resources:
-
-| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
-|---------------------|--------|------------|
-| Antibodies | | |
-| Rabbit anti-FOXO4 | Abcam | Cat#ab12345 |
-| Chemicals | | |
-| Doxorubicin | Sigma-Aldrich | Cat#D1515 |
-| Cell Lines | | |
-| IMR90 | ATCC | CCL-186 |
-
----
-
-## Figures
-
-### Figure Philosophy
-
-Cell papers are **figure-heavy** with extensive multi-panel figures:
-
-- **6-8 main figures** typical
-- **Multi-panel format**: 6-12 panels per figure common
-- **Data-dense**: Comprehensive experimental support
-- **Extended Data**: Supplementary figures for additional validation
-
-### Panel Labeling
-
-Panels labeled with lowercase letters: **(A)**, **(B)**, **(C)**
-
-### Figure Legend Format
-
-```
-Figure 3. FOXO4 Sequesters p53 in the Nucleus of Senescent Cells
-
-(A) Immunofluorescence microscopy of p53 (green) and FOXO4 (red) in 
-proliferating (left) and senescent (right) IMR90 cells. DAPI (blue) 
-marks nuclei. Scale bar, 10 μm.
-
-(B) Quantification of nuclear p53 intensity in proliferating versus 
-senescent cells. Data represent mean ± SEM; n = 3 biological replicates, 
->100 cells per condition. ***p < 0.001, two-tailed Student's t test.
-
-(C and D) Co-immunoprecipitation of FOXO4 and p53 in proliferating (C) 
-and senescent (D) cell lysates. IgG, immunoglobulin G control.
-
-(E) Proximity ligation assay for FOXO4-p53 interaction. Red dots indicate 
-interaction events. Scale bar, 10 μm.
-
-(F) Model of FOXO4-mediated p53 sequestration in senescent cells.
-
-See also Figure S3 and Table S2.
-```
-
----
-
-## References
-
-### Citation Style
-
-- **Author-year format**: (Smith et al., 2023) or Smith et al. (2023)
-- **Multiple citations**: (Smith et al., 2020; Jones et al., 2021)
-- **Two authors**: (Smith and Jones, 2023)
-- **Three or more**: (Smith et al., 2023)
-
-### Reference Format
-
-```
-Baker, D.J., Wijshake, T., Tchkonia, T., LeBrasseur, N.K., Childs, B.G., 
-van de Sluis, B., Kirkland, J.L., and van Deursen, J.M. (2011). Clearance 
-of p16Ink4a-positive senescent cells delays ageing-associated disorders. 
-Nature 479, 232–236.
-```
-
----
-
-## Cell Press Journal Comparison
-
-| Journal | Focus | Article Length | Figures |
-|---------|-------|---------------|---------|
-| **Cell** | Breakthrough biology | Long | 7-8 main + ED |
-| **Neuron** | Neuroscience | Long | 6-8 main |
-| **Immunity** | Immunology | Medium-Long | 6-7 main |
-| **Molecular Cell** | Molecular mechanisms | Medium | 5-7 main |
-| **Developmental Cell** | Development | Medium | 5-7 main |
-| **Cell Reports** | Solid science | Medium | 4-6 main |
-
----
-
-## Common Mistakes
-
-1. **Insufficient mechanism**: Describing what happens without how
-2. **Under-controlled experiments**: Missing key controls
-3. **Weak phenotype validation**: Single approach instead of multiple
-4. **Missing in vivo work**: Cell papers often expect animal studies
-5. **Incomplete figure panels**: Not showing all relevant conditions
-6. **Forgetting graphical abstract**: Required element
-7. **Exceeding highlight character limits**: ≤85 characters per bullet
-
----
-
-## Pre-Submission Checklist
-
-### Required Elements (verify for the exact journal and article type)
-- [ ] Graphical abstract, if required
-- [ ] Highlights, eTOC blurb, and Summary within the current limits
-- [ ] Key Resources Table and STAR Methods components, if required
-- [ ] Limitations of the Study
-- [ ] Resource Availability and Lead Contact information
-- [ ] Declaration of generative AI and AI-assisted technologies, when applicable
-
-### Content
-- [ ] Mechanistic depth throughout
-- [ ] Multiple complementary approaches
-- [ ] In vivo validation (if applicable)
-- [ ] Declarative subheadings
-- [ ] Comprehensive figure panels
-
-### Style
-- [ ] Technical precision in terminology
-- [ ] Author-year citations
-- [ ] Figure legends complete and standalone
-- [ ] STAR Methods properly formatted
-
----
-
-## See Also
-
-- `venue_writing_styles.md` - Master style overview
-- `journals_formatting.md` - Technical formatting requirements
-- `nature_science_style.md` - Comparison with Nature/Science style
-

package/skills/venue-templates/references/conferences_formatting.md

@@ -1,175 +0,0 @@
-# Conference Formatting Requirements
-
-Current-year conference rules change independently by track. Use this guide to find the authoritative source and to understand the scope of the rule; do not carry a page limit or style file into another year.
-
-**Reviewed:** 2026-07-20
-
-## How to Use This Guide
-
-For every submission, record:
-
-1. conference year and track;
-2. initial, rebuttal, or camera-ready stage;
-3. official author-instruction URL and date checked;
-4. page-limit scope, including references and appendices;
-5. anonymity and external-link policy; and
-6. exact official template package.
-
-Official instructions and files override every summary below.
-
-## Verified 2026 ML and Vision Snapshots
-
-### NeurIPS 2026 — Main Track
-
-**Official sources**
-
-- Call for Papers: https://neurips.cc/Conferences/2026/CallForPapers
-- Main Track Handbook: https://neurips.cc/Conferences/2026/MainTrackHandbook
-- Official formatting package: linked from the Call for Papers
-
-**Initial submission**
-
-- Up to **9 content pages**, including figures.
-- Additional pages containing acknowledgments, references, the required paper checklist, and optional technical appendices do not count as content pages.
-- Omit both the `final` and `preprint` style options; the official style then anonymizes the submission and adds line numbers.
-- Do not include acknowledgments in the anonymized submission.
-- The **NeurIPS Paper Checklist is required**; omitting it can cause desk rejection.
-- Technical appendices may be included after the references. Reviewers are not required to rely on them.
-
-**Template rule**
-
-Use the exact NeurIPS 2026 package. The bundled `assets/journals/neurips_article.tex` is only a wrapper and requires the official `neurips_2026.sty` and checklist files.
-
-### ICML 2026 — Main Track
-
-**Official sources**
-
-- Author Instructions: https://icml.cc/Conferences/2026/AuthorInstructions
-- Call for Papers: https://icml.cc/Conferences/2026/CallForPapers
-- Official style package: https://media.icml.cc/Conferences/ICML2026/Styles/icml2026.zip
-
-**Initial submission**
-
-- Main body: up to **8 pages**.
-- References and appendices may use additional pages and remain in the same PDF.
-- Submissions must use LaTeX, be anonymized, and follow the official style.
-- The camera-ready version permits one extra main-body page.
-- Material essential to evaluation belongs in the main body; reviewers may decline to read appendices or separate supplements.
-
-### ICLR 2026
-
-**Official source**
-
-- Author Guide: https://iclr.cc/Conferences/2026/AuthorGuide
-
-**Initial submission**
-
-- Main text: up to **9 pages**.
-- References do not count toward the limit.
-- Appendices may use additional pages, but reviewers are not required to read them.
-- Submissions are double blind; identifying information in the paper or supplement can cause desk rejection.
-- Use the `iclr2026` package linked by the Author Guide.
-
-**Later stages**
-
-- The discussion/rebuttal and camera-ready limit increases to **10 main-text pages**.
-- Do not apply that later-stage allowance to the initial submission.
-
-### CVPR 2026
-
-**Official source**
-
-- Author Guidelines: https://cvpr.thecvf.com/Conferences/2026/AuthorGuidelines
-
-**Initial submission**
-
-- Main paper: up to **8 pages**, including figures and tables.
-- Additional pages may contain cited references only.
-- Use the official CVPR 2026 author kit linked by the Author Guidelines.
-- Papers must be anonymized. Identifying acknowledgments, grant IDs, videos, attached papers, or external links can violate anonymity.
-- External links that expand submitted content or bypass length restrictions are prohibited.
-
-**Rebuttal**
-
-- The rebuttal is a one-page PDF using the rebuttal template from the author kit.
-- It must remain anonymous and may not add external material.
-
-## Other Conference Families
-
-The following links are discovery starting points, not cached requirements.
-
-| Venue/family | Official starting point | Template rule |
-|---|---|---|
-| AAAI | https://aaai.org/conference/aaai/ | Use the target year's author kit |
-| IJCAI | https://www.ijcai.org/ | Use the target year's call and style |
-| ACL / ARR | https://aclrollingreview.org/ | Check ARR submission requirements and the committing venue |
-| EMNLP | https://www.emnlp.org/ | Check the current call and ACL style package |
-| ACM CHI | https://chi.acm.org/ | Check the current papers track and ACM workflow |
-| ACM SIGKDD | https://kdd.org/ | Check the exact track; limits differ |
-| ACM SIGIR | https://sigir.org/ | Check the target year's call |
-| USENIX Security | https://www.usenix.org/conference/usenixsecurity | Check the current submission cycle and artifact rules |
-| ISMB | https://www.iscb.org/ismb | Check the proceedings track and journal instructions |
-| RECOMB | https://www.recomb.org/ | Check the target year's Springer/author kit |
-| PSB | https://psb.stanford.edu/ | Check the current author instructions |
-| IEEE conferences | https://conferences.ieeeauthorcenter.ieee.org/ | Use the conference-selected IEEE template |
-| ICRA | https://www.ieee-ras.org/conferences-workshops/fully-sponsored/icra | Check the current author kit and page charges |
-
-Do not assume that last year's page limit, review model, supplement policy, or class options survived unchanged.
-
-## Official Template Workflow
-
-1. Download the package from the conference's official author page.
-2. Keep all `.sty`, `.cls`, bibliography, and checklist files together.
-3. Compile the sample before editing.
-4. Copy the sample and replace content without changing layout commands.
-5. Preserve submission mode for review; enable camera-ready options only after acceptance.
-6. Re-download the package if the organizers announce a revision.
-
-Avoid unofficial mirrors when an official package exists. Do not rename an old style file to a new year.
-
-## Blind-Review Checklist
-
-Check the manuscript, supplement, source archive, PDF metadata, figures, and linked resources.
-
-- Remove names, affiliations, emails, acknowledgments, grant numbers, and institution-identifying text when required.
-- Follow the venue's self-citation policy; do not automatically replace every self-citation with “Anonymous.”
-- Remove identifying paths, usernames, comments, Git metadata, document properties, and image metadata.
-- Use only external links permitted by the current policy.
-- Ensure code and data packages are anonymized if submitted for review.
-- Do not disclose the submission's venue status where the conference prohibits it.
-
-## Page-Limit Interpretation
-
-“Eight pages” is incomplete without scope. Record whether the limit applies to:
-
-- main text only;
-- figures and tables;
-- acknowledgments;
-- references;
-- appendices;
-- checklists or impact statements; and
-- the combined PDF or a separate supplement.
-
-When using `scripts/validate_format.py`, supply `--content-pages` after manually counting according to this scope. Total PDF pages alone cannot establish compliance.
-
-## Supplementary Material
-
-- Put claims essential to acceptance in the main paper.
-- Treat appendices as optional reading unless the current instructions say otherwise.
-- Apply the same anonymity rules to supplements.
-- Check file count, type, and size limits.
-- Do not use links or supplements to evade the main-paper limit.
-- Confirm whether code/data uploads share the paper deadline.
-
-## Camera-Ready Preparation
-
-After acceptance:
-
-1. switch to the official final/camera-ready mode;
-2. add authors and permitted acknowledgments;
-3. apply the camera-ready page allowance, if any;
-4. complete rights, licensing, accessibility, and metadata forms;
-5. include only accepted and permitted supplementary material; and
-6. inspect the publisher or proceedings proof.
-
-Submission and camera-ready rules are different contracts. Re-verify both.