Referee Review

Referee Review — 审稿人专用审稿技能

定位

作为期刊审稿人（referee）系统评价他人稿件。与以下 skills 互补：

• paper-review：投稿前自审工具（检查自己论文格式）
• academic-craft：写作质量诊断（6维度 A/B/C 打分）
• referee-review（本 skill）：审别人的稿件，生成标准审稿信

触发场景

• "帮我审这篇论文" / "作为审稿人评价这篇稿件"
• "生成审稿意见" / "写审稿信"
• "评价这篇论文的方法论/统计分析"
• "审查论文的可复现性"
• Reviewing scientific manuscripts as a referee for journals

适用期刊

物理/光学领域常见期刊：PRL, PRA/B/D, Optica, Light: Sci. Appl., APL, IEEE Photonics, Nat. Photonics, Sci. Rep.

Peer Review Workflow

Conduct peer review systematically through the following stages, adapting depth and focus based on the manuscript type and discipline.

Stage 1: Initial Assessment

Begin with a high-level evaluation to determine the manuscript's scope, novelty, and overall quality.

Key Questions:

• What is the central research question or hypothesis?
• What are the main findings and conclusions?
• Is the work scientifically sound and significant?
• Is the work appropriate for the intended venue?
• Are there any immediate major flaws that would preclude publication?

Output: Brief summary (2-3 sentences) capturing the manuscript's essence and initial impression.

Stage 2: Detailed Section-by-Section Review

Conduct a thorough evaluation of each manuscript section, documenting specific concerns and strengths.

Abstract and Title

• Accuracy: Does the abstract accurately reflect the study's content and conclusions?
• Clarity: Is the title specific, accurate, and informative?
• Completeness: Are key findings and methods summarized appropriately?
• Accessibility: Is the abstract comprehensible to a broad scientific audience?

Introduction

• Context: Is the background information adequate and current?
• Rationale: Is the research question clearly motivated and justified?
• Novelty: Is the work's originality and significance clearly articulated?
• Literature: Are relevant prior studies appropriately cited?
• Objectives: Are research aims/hypotheses clearly stated?

Methods

• Reproducibility: Can another researcher replicate the study from the description provided?
• Rigor: Are the methods appropriate for addressing the research questions?
• Detail: Are protocols, reagents, equipment, and parameters sufficiently described?
• Ethics: Are ethical approvals, consent, and data handling properly documented?
• Statistics: Are statistical methods appropriate, clearly described, and justified?
• Validation: Are controls, replicates, and validation approaches adequate?

Critical elements to verify:

• Sample sizes and power calculations
• Randomization and blinding procedures
• Inclusion/exclusion criteria
• Data collection protocols
• Computational methods and software versions
• Statistical tests and correction for multiple comparisons

Results

• Presentation: Are results presented logically and clearly?
• Figures/Tables: Are visualizations appropriate, clear, and properly labeled?
• Statistics: Are statistical results properly reported (effect sizes, confidence intervals, p-values)?
• Objectivity: Are results presented without over-interpretation?
• Completeness: Are all relevant results included, including negative results?
• Reproducibility: Are raw data or summary statistics provided?

Common issues to identify:

• Selective reporting of results
• Inappropriate statistical tests
• Missing error bars or measures of variability
• Over-fitting or circular analysis
• Batch effects or confounding variables
• Missing controls or validation experiments

Discussion

• Interpretation: Are conclusions supported by the data?
• Limitations: Are study limitations acknowledged and discussed?
• Context: Are findings placed appropriately within existing literature?
• Speculation: Is speculation clearly distinguished from data-supported conclusions?
• Significance: Are implications and importance clearly articulated?
• Future directions: Are next steps or unanswered questions discussed?

Red flags:

• Overstated conclusions
• Ignoring contradictory evidence
• Causal claims from correlational data
• Inadequate discussion of limitations
• Mechanistic claims without mechanistic evidence

References

• Completeness: Are key relevant papers cited?
• Currency: Are recent important studies included?
• Balance: Are contrary viewpoints appropriately cited?
• Accuracy: Are citations accurate and appropriate?
• Self-citation: Is there excessive or inappropriate self-citation?

Stage 3: Methodological and Statistical Rigor

Evaluate the technical quality and rigor of the research with particular attention to common pitfalls.

Statistical Assessment:

• Are statistical assumptions met (normality, independence, homoscedasticity)?
• Are effect sizes reported alongside p-values?
• Is multiple testing correction applied appropriately?
• Are confidence intervals provided?
• Is sample size justified with power analysis?
• Are parametric vs. non-parametric tests chosen appropriately?
• Are missing data handled properly?
• Are exploratory vs. confirmatory analyses distinguished?

Experimental Design:

• Are controls appropriate and adequate?
• Is replication sufficient (biological and technical)?
• Are potential confounders identified and controlled?
• Is randomization properly implemented?
• Are blinding procedures adequate?
• Is the experimental design optimal for the research question?

Computational/Bioinformatics:

• Are computational methods clearly described and justified?
• Are software versions and parameters documented?
• Is code made available for reproducibility?
• Are algorithms and models validated appropriately?
• Are assumptions of computational methods met?
• Is batch correction applied appropriately?

Stage 4: Reproducibility and Transparency

Assess whether the research meets modern standards for reproducibility and open science.

Data Availability:

• Are raw data deposited in appropriate repositories?
• Are accession numbers provided for public databases?
• Are data sharing restrictions justified (e.g., patient privacy)?
• Are data formats standard and accessible?

Code and Materials:

• Is analysis code made available (GitHub, Zenodo, etc.)?
• Are unique materials available or described sufficiently for recreation?
• Are protocols detailed in sufficient depth?

Reporting Standards:

• Does the manuscript follow discipline-specific reporting guidelines (PRISMA for systematic reviews)?
• Are all experimental parameters sufficient for replication?
• Are all elements of the appropriate checklist addressed?

Stage 5: Figure and Data Presentation

Evaluate the quality, clarity, and integrity of data visualization.

Quality Checks:

• Are figures high resolution and clearly labeled?
• Are axes properly labeled with units?
• Are error bars defined (SD, SEM, CI)?
• Are statistical significance indicators explained?
• Are color schemes appropriate and accessible (colorblind-friendly)?
• Are scale bars included for images?
• Is data visualization appropriate for the data type?

Integrity Checks:

• Are there signs of image manipulation (duplications, splicing, inconsistent scale bars)?
• Are representative images/measurements truly representative?
• Are all conditions shown (no selective presentation)?
• Are spectra/plots showing raw data or only processed results?

Clarity:

• Can figures stand alone with their legends?
• Is the message of each figure immediately clear?
• Are there redundant figures or panels?
• Would data be better presented as tables or figures?

Stage 6: 研究诚信与光学实验特有检查

研究诚信（通用）：

• 是否存在数据伪造或篡改的嫌疑？
• 作者署名是否合理？
• 利益冲突是否声明？
• 基金来源是否披露？
• 是否存在抄袭或重复发表？

光学/物理实验特有审查项：

• 激光参数是否完整报告？（波长、功率、脉宽、重复频率、光束质量 M²）
• 光学系统校准是否描述？（波长校准、功率计校准、光路对准方法）
• 探测器参数是否明确？（类型、带宽、NEP、响应率、线性范围）
• 实验环境条件是否说明？（温度、湿度、振动隔离、暗室条件）
• 样品制备是否可复现？（材料来源、纯度、厚度、表面处理）
• 数值模拟参数是否完整？（网格分辨率、收敛判据、边界条件、软件版本）
• 误差分析是否系统化？（系统误差 vs 随机误差、不确定度传播、误差棒含义）
• 光谱/图像数据是否提供原始格式？（不只是处理后的图，有无原始数据可用性声明）
• 理论假设的适用范围是否明确讨论？

Stage 7: Writing Quality and Clarity

Assess the manuscript's clarity, organization, and accessibility.

Structure and Organization:

• Is the manuscript logically organized?
• Do sections flow coherently?
• Are transitions between ideas clear?
• Is the narrative compelling and clear?

Writing Quality:

• Is the language clear, precise, and concise?
• Are jargon and acronyms minimized and defined?
• Is grammar and spelling correct?
• Are sentences unnecessarily complex?
• Is the passive voice overused?

Accessibility:

• Can a non-specialist understand the main findings?
• Are technical terms explained?
• Is the significance clear to a broad audience?

Structuring Peer Review Reports

Organize feedback in a hierarchical structure that prioritizes issues and provides actionable guidance.

Summary Statement

Provide a concise overall assessment (1-2 paragraphs):

• Brief synopsis of the research
• Overall recommendation (accept, minor revisions, major revisions, reject)
• Key strengths (2-3 bullet points)
• Key weaknesses (2-3 bullet points)
• Bottom-line assessment of significance and soundness

Major Comments

List critical issues that significantly impact the manuscript's validity, interpretability, or significance. Number these sequentially for easy reference.

Major comments typically include:

• Fundamental methodological flaws
• Inappropriate statistical analyses
• Unsupported or overstated conclusions
• Missing critical controls or experiments
• Serious reproducibility concerns
• Major gaps in literature coverage
• Ethical concerns

For each major comment:

1. Clearly state the issue
2. Explain why it's problematic
3. Suggest specific solutions or additional experiments
4. Indicate if addressing it is essential for publication

Minor Comments

List less critical issues that would improve clarity, completeness, or presentation. Number these sequentially.

Minor comments typically include:

• Unclear figure labels or legends
• Missing methodological details
• Typographical or grammatical errors
• Suggestions for improved data presentation
• Minor statistical reporting issues
• Supplementary analyses that would strengthen conclusions
• Requests for clarification

For each minor comment:

1. Identify the specific location (section, paragraph, figure)
2. State the issue clearly
3. Suggest how to address it

Specific Line-by-Line Comments (Optional)

For manuscripts requiring detailed feedback, provide section-specific or line-by-line comments:

• Reference specific page/line numbers or sections
• Note factual errors, unclear statements, or missing citations
• Suggest specific edits for clarity

Questions for Authors

List specific questions that need clarification:

• Methodological details that are unclear
• Seemingly contradictory results
• Missing information needed to evaluate the work
• Requests for additional data or analyses

Tone and Approach

Maintain a constructive, professional, and collegial tone throughout the review.

Best Practices:

• Be constructive: Frame criticism as opportunities for improvement
• Be specific: Provide concrete examples and actionable suggestions
• Be balanced: Acknowledge strengths as well as weaknesses
• Be respectful: Remember that authors have invested significant effort
• Be objective: Focus on the science, not the scientists
• Be thorough: Don't overlook issues, but prioritize appropriately
• Be clear: Avoid ambiguous or vague criticism

Avoid:

• Personal attacks or dismissive language
• Sarcasm or condescension
• Vague criticism without specific examples
• Requesting unnecessary experiments beyond the scope
• Demanding adherence to personal preferences vs. best practices
• Revealing your identity if reviewing is double-blind

Special Considerations by Manuscript Type

Original Research Articles

• Emphasize rigor, reproducibility, and novelty
• Assess significance and impact
• Verify that conclusions are data-driven
• Check for complete methods and appropriate controls

Reviews and Meta-Analyses

• Evaluate comprehensiveness of literature coverage
• Assess search strategy and inclusion/exclusion criteria
• Verify systematic approach and lack of bias
• Check for critical analysis vs. mere summarization
• For meta-analyses, evaluate statistical approach and heterogeneity

Methods Papers

• Emphasize validation and comparison to existing methods
• Assess reproducibility and availability of protocols/code
• Evaluate improvements over existing approaches
• Check for sufficient detail for implementation

Short Reports/Letters

• Adapt expectations for brevity
• Ensure core findings are still rigorous and significant
• Verify that format is appropriate for findings

Preprints

• Recognize that these have not undergone formal peer review
• May be less polished than journal submissions
• Still apply rigorous standards for scientific validity
• Consider providing constructive feedback to help authors improve before journal submission

Presentations and Slide Decks

⚠️ CRITICAL: For presentations, NEVER read the PDF directly. ALWAYS convert to images first.

When reviewing scientific presentations (PowerPoint, Beamer, slide decks):

Mandatory Image-Based Review Workflow

NEVER attempt to read presentation PDFs directly - this causes buffer overflow errors and doesn't show visual formatting issues.

Required Process:

1. Convert PDF to images using Python:

   python skills/scientific-slides/scripts/pdf_to_images.py presentation.pdf review/slide --dpi 150
   # Creates: review/slide-001.jpg, review/slide-002.jpg, etc.
   

2. Read and inspect EACH slide image file sequentially
3. Document issues with specific slide numbers
4. Provide feedback on visual formatting and content

Print when starting review:

[HH:MM:SS] PEER REVIEW: Presentation detected - converting to images for review
[HH:MM:SS] PDF REVIEW: NEVER reading PDF directly - using image-based inspection

Presentation-Specific Evaluation Criteria

Visual Design and Readability:

• Text is large enough (minimum 18pt, ideally 24pt+ for body text)
• High contrast between text and background (4.5:1 minimum, 7:1 preferred)
• Color scheme is professional and colorblind-accessible
• Consistent visual design across all slides
• White space is adequate (not cramped)
• Fonts are clear and professional

Layout and Formatting (Check EVERY Slide Image):

• No text overflow or truncation at slide edges
• No element overlaps (text over images, overlapping shapes)
• Titles are consistently positioned
• Content is properly aligned
• Bullets and text are not cut off
• Figures fit within slide boundaries
• Captions and labels are visible and readable

Content Quality:

• One main idea per slide (not overloaded)
• Minimal text (3-6 bullets per slide maximum)
• Bullet points are concise (5-7 words each)
• Figures are simplified and clear (not copy-pasted from papers)
• Data visualizations have large, readable labels
• Citations are present and properly formatted
• Results/data slides dominate the presentation (40-50% of content)

Structure and Flow:

• Clear narrative arc (introduction → methods → results → discussion)
• Logical progression between slides
• Slide count appropriate for talk duration (~1 slide per minute)
• Title slide includes authors, affiliation, date
• Introduction cites relevant background literature (3-5 papers)
• Discussion cites comparison papers (3-5 papers)
• Conclusions slide summarizes key findings
• Acknowledgments/funding slide at end

Scientific Content:

• Research question clearly stated
• Methods adequately summarized (not excessive detail)
• Results presented logically with clear visualizations
• Statistical significance indicated appropriately
• Conclusions supported by data shown
• Limitations acknowledged where appropriate
• Future directions or broader impact discussed

Common Presentation Issues to Flag:

Critical Issues (Must Fix):

• Text overflow making content unreadable
• Font sizes too small (<18pt)
• Element overlaps obscuring data
• Insufficient contrast (text hard to read)
• Figures too complex or illegible
• No citations (completely unsupported claims)
• Slide count drastically mismatched to duration

Major Issues (Should Fix):

• Inconsistent design across slides
• Too much text (walls of text, not bullets)
• Poorly simplified figures (axis labels too small)
• Cramped layout with insufficient white space
• Missing key structural elements (no conclusion slide)
• Poor color choices (not colorblind-safe)
• Minimal results content (<30% of slides)

Minor Issues (Suggestions for Improvement):

• Could use more visuals/diagrams
• Some slides slightly text-heavy
• Minor alignment inconsistencies
• Could benefit from more white space
• Additional citations would strengthen claims
• Color scheme could be more modern

Review Report Format for Presentations

Summary Statement:

• Overall impression of presentation quality
• Appropriateness for target audience and duration
• Key strengths (visual design, content, clarity)
• Key weaknesses (formatting issues, content gaps)
• Recommendation (ready to present, minor revisions, major revisions)

Layout and Formatting Issues (By Slide Number):

Slide 3: Text overflow - bullet point 4 extends beyond right margin
Slide 7: Element overlap - figure overlaps with caption text
Slide 12: Font size - axis labels too small to read from distance
Slide 18: Alignment - title not centered

Content and Structure Feedback:

• Adequacy of background context and citations
• Clarity of research question and objectives
• Quality of methods summary
• Effectiveness of results presentation
• Strength of conclusions and implications

Design and Accessibility:

• Overall visual appeal and professionalism
• Color contrast and readability
• Colorblind accessibility
• Consistency across slides

Timing and Scope:

• Whether slide count matches intended duration
• Appropriate level of detail for talk type
• Balance between sections

Example Image-Based Review Process

[14:30:00] PEER REVIEW: Starting review of presentation
[14:30:05] PEER REVIEW: Presentation detected - converting to images
[14:30:10] PDF REVIEW: Running pdf_to_images.py on presentation.pdf
[14:30:15] PDF REVIEW: Converted 25 slides to images in review/ directory
[14:30:20] PDF REVIEW: Inspecting slide 1/25 - title slide
[14:30:25] PDF REVIEW: Inspecting slide 2/25 - introduction
...
[14:35:40] PDF REVIEW: Inspecting slide 25/25 - acknowledgments
[14:35:45] PDF REVIEW: Completed image-based review
[14:35:50] PEER REVIEW: Found 8 layout issues, 3 content issues
[14:35:55] PEER REVIEW: Generating structured feedback by slide number

Remember: For presentations, the visual inspection via images is MANDATORY. Never attempt to read presentation PDFs as text - it will fail and miss all visual formatting issues.

Resources

This skill includes reference materials to support comprehensive peer review:

references/reporting_standards.md

Guidelines for major reporting standards across disciplines (CONSORT, PRISMA, ARRIVE, MIAME, STROBE, etc.) to evaluate completeness of methods and results reporting.

references/common_issues.md

Catalog of frequent methodological and statistical issues encountered in peer review, with guidance on identifying and addressing them.

Final Checklist

Before finalizing the review, verify:

• Summary statement clearly conveys overall assessment
• Major concerns are clearly identified and justified
• Suggested revisions are specific and actionable
• Minor issues are noted but properly categorized
• Statistical methods have been evaluated
• Reproducibility and data availability assessed
• Ethical considerations verified
• Figures and tables evaluated for quality and integrity
• Writing quality assessed
• Tone is constructive and professional throughout
• Review is thorough but proportionate to manuscript scope
• Recommendation is consistent with identified issues

审稿信模板（中英双语）

审稿信是审稿人给编辑和作者的正式意见。使用以下模板，按需填写。

English Template

Referee Report
Manuscript: [Title]
Journal: [Journal Name]
Date: [YYYY-MM-DD]

=== Summary ===
[2-3 sentences summarizing the paper's contribution]

=== General Assessment ===
Recommendation: [Accept / Minor Revision / Major Revision / Reject]

Strengths:
1. [Key strength]
2. [Key strength]

Weaknesses:
1. [Key weakness]
2. [Key weakness]

=== Major Comments ===
1. [Specific issue with location and suggested fix]
2. ...

=== Minor Comments ===
1. [Specific issue with location]
2. ...

=== Questions for Authors ===
1. [Clarification needed]
2. ...

中文模板

审稿意见
稿件: [标题]
期刊: [期刊名]
日期: [YYYY-MM-DD]

=== 概述 ===
[2-3 句话概括论文贡献]

=== 总体评价 ===
建议: [接收 / 小修 / 大修 / 拒稿]

优点:
1. [核心优点]
2. [核心优点]

不足:
1. [核心问题]
2. [核心问题]

=== 主要意见 ===
1. [具体问题，标注位置和修改建议]
2. ...

=== 次要意见 ===
1. [具体问题，标注位置]
2. ...

=== 致作者的问题 ===
1. [需要澄清的问题]
2. ...

光学/物理期刊特有审稿要点

PRL (Physical Review Letters) 审稿关注

• 是否解释了对广泛物理学界的重要性（broad interest）
• 创新性是否足以支撑 Letter 级别
• 理论推导是否自洽，假设是否合理
• 实验证据是否支持核心结论
• 长度限制内是否完整表达了关键信息

Optica/Light: Science & Applications 审稿关注

• 光学工程/应用价值是否明确
• 与现有技术的定量对比是否充分
• 实验方案是否考虑了实际应用场景
• 是否讨论了技术局限性和改进方向

APL (Applied Physics Letters) 审稿关注

• 应用量子物理/光学的新颖性
• 实验可复现性（参数是否充分）
• 与理论预测的对比是否定量
• 实际器件/系统性能指标是否完整

统计审稿快速检查（物理实验适用）

• 误差棒含义是否说明（SD / SEM / 95% CI）
• 样本量/测量次数是否足够
• 是否报告了效应量（不只是 p-value）
• 多重比较是否校正（如适用）
• 拟合参数是否有不确定度
• 理论曲线与实验数据的残差是否展示
• 系统误差是否讨论

定制化自 K-Dense scientific-agent-skills peer-review skill 适配光学 PhD 审稿需求 — v1.0-customized