Paper Writer

Overview

Section-by-section academic writing skill that generates publication-quality content by matching section content points with relevant reference paragraphs through semantic similarity, then writing in fluent academic prose.

Core scientific writing skill combining semantic matching with full academic manuscript capabilities: IMRAD structure, citation styles (APA/AMA/Vancouver/IEEE/Chicago), reporting guidelines (CONSORT/STROBE/PRISMA), figures/tables, and venue-specific formatting.

Critical Principle: Always write in full paragraphs with flowing prose. Never submit bullet points in scientific papers.

When to Use

• •Requirements document parsed with references by section
• •Reference fulltext content available
• •Need to generate paper content section-by-section
• •Need semantic matching between content points and reference paragraphs
• •Need full academic manuscript capabilities (journal submission, reporting guidelines, etc.)

Writing Principles

1. Section-by-Section Writing Process

For each section in order:

1. •Review section structure - Title, subsections, content points
2. •Review reference content - Read fulltext paragraphs for each reference
3. •Semantic matching - Identify which reference paragraphs match each content point
4. •Template selection - Use first reference as primary template for structure
5. •Write prose - Expand content points using matched reference paragraphs as template
6. •Add supporting citations - Use semantic search results for additional support
7. •Format appropriately - Apply venue-specific or standard academic formatting

2. Semantic Matching Rules

Matching Process:

Key Insight: Reference headings often don't contain topic information. Match by paragraph content, not section titles.

3. Template Selection Rules

• •Primary template: First listed reference for the section
• •Secondary references: All other listed references (used for comparison/supplement)
• •Supplementary support: Semantic search results for additional citations

4. Core Writing Principles

Clarity:

• •Use precise, unambiguous language
• •Define technical terms and abbreviations at first use
• •Maintain logical flow within and between paragraphs
• •Use active voice when appropriate for clarity

Conciseness:

• •Eliminate redundant words and phrases
• •Favor shorter sentences (15-20 words average)
• •Remove unnecessary qualifiers
• •Respect word limits strictly

Accuracy:

• •Report exact values with appropriate precision
• •Use consistent terminology throughout
• •Distinguish between observations and interpretations
• •Acknowledge uncertainty appropriately

Objectivity:

• •Present results without bias
• •Avoid overstating findings or implications
• •Acknowledge conflicting evidence
• •Maintain professional, neutral tone

5. Citation Management

Major Citation Styles:

• •APA (Author, Year): Common in social sciences, natural sciences
• •AMA: Numbered superscript citations, common in medicine
• •Vancouver: Numbered citations in square brackets [1], biomedical standard
• •IEEE: Numbered square brackets [1], engineering and computer science
• •Chicago: Notes-bibliography or author-date, humanities and sciences

Best Practices:

• •Cite primary sources when possible
• •Include recent literature (last 5-10 years for active fields)
• •Balance citation distribution across introduction and discussion
• •Integrate citations naturally within sentences, not as lists
• •Verify all citations against original sources

6. Manuscript Structure (IMRAD)

Standard Sections:

• •Introduction: Establish research context, identify gaps, state objectives
• •Related Work: Review relevant literature systematically
• •Methods: Detail study design, populations, procedures, and analysis
• •Results: Present findings objectively without interpretation
• •Discussion: Interpret results, acknowledge limitations, propose future directions
• •Conclusion: Summarize key contributions and implications

For Chinese academic papers:

• •摘要 (Abstract): Concise summary in Chinese
• •关键词 (Keywords): 3-5 terms
• •第X章 structure following Chinese thesis standards

7. Reporting Guidelines by Study Type

Ensure completeness and transparency by following established reporting standards:

8. Figures and Tables

When to Use Tables vs. Figures:

• •Tables: Precise numerical data, complex datasets, multiple variables requiring exact values
• •Figures: Trends, patterns, relationships, comparisons best understood visually

Design Principles:

• •Make each table/figure self-explanatory with complete captions
• •Use consistent formatting and terminology across all display items
• •Label all axes, columns, and rows with units
• •Include sample sizes (n) and statistical annotations
• •Follow the "one table/figure per 1000 words" guideline
• •Avoid duplicating information between text, tables, and figures

Common Figure Types:

• •Bar graphs: Comparing discrete categories
• •Line graphs: Showing trends over time
• •Scatterplots: Displaying correlations
• •Box plots: Showing distributions and outliers
• •Heatmaps: Visualizing matrices and patterns

9. Field-Specific Terminology

Biomedical and Clinical Sciences:

• •Use precise anatomical and clinical terminology
• •Use "patients" for clinical studies, "participants" for community-based research
• •Report lab values with standard SI units
• •Follow standardized disease nomenclature (ICD, DSM, SNOMED-CT)

Molecular Biology and Genetics:

• •Use italics for gene symbols (e.g., TP53), regular font for proteins (e.g., p53)
• •Follow species-specific gene nomenclature
• •Specify organism names in full at first mention

Chemistry and Pharmaceutical Sciences:

• •Follow IUPAC nomenclature for chemical compounds
• •Report concentrations with appropriate units (mM, μM, nM, or % w/v, v/v)
• •Use terms like "bioavailability," "pharmacokinetics," "IC50" consistently

Physics and Engineering:

• •Follow SI units consistently
• •Specify equipment with model numbers and manufacturers when relevant
• •Use standard notation for physical quantities

General Principles:

• •Define abbreviations at first use: "messenger RNA (mRNA)"
• •Maintain consistency throughout the document
• •Match terminology to audience expertise

10. Journal-Specific Formatting

Adapt manuscripts to journal requirements:

• •Follow author guidelines for structure, length, and format
• •Apply journal-specific citation styles
• •Meet figure/table specifications (resolution, file formats, dimensions)
• •Include required statements (funding, conflicts of interest, data availability, ethical approval)
• •Adhere to word limits for each section

Input Format

{
  "paper_title": "Paper Title",
  "language": "zh-CN | en-US",
  "citation_style": "APA | AMA | Vancouver | IEEE | Chicago",
  "sections": [
    {
      "title": "第1章 绪论",
      "subsections": [
        {
          "title": "1.1 研究背景与意义",
          "content_points": [
            "日盲紫外探测在军事和民用领域的重要应用",
            "现有技术的局限性"
          ],
          "references": [
            {"title": "Reference Title 1", "key": "ZoteroKey1"},
            {"title": "Reference Title 2", "key": "ZoteroKey2"}
          ]
        }
      ]
    }
  ],
  "supplementary_references": [],
  "journal_format": "standard | nature | science | cell | ieee | ...",
  "reporting_guideline": "CONSORT | STROBE | PRISMA | ..."
}

Processing Steps

1. •Process sections in order - Start from first chapter to last
2. •For each section: a. Review content points - Understand what needs to be written b. Fetch reference fulltexts - Call zotero_get_item_fulltext for each reference key c. Parse and split fulltext - Split into paragraphs, ignore headings d. Semantic match - Match each content point to relevant paragraphs e. Select template - Use first reference as primary template f. Write prose - Convert content points to full paragraphs using two-stage process g. Add citations - Reference [1], [2] based on matched sources h. Apply formatting - Use venue-specific or standard academic formatting
3. •Compile output - Combine all sections into complete paper

Two-Stage Writing Process

Stage 1: Create Section Outlines with Key Points

When starting a new section:

1. •Review the provided content points
2. •Organize the main arguments or findings to present
3. •Identify key studies to cite from matched references
4. •Plan logical flow and organization

Stage 2: Convert Key Points to Full Paragraphs

Once the outline is complete, expand each point into proper prose:

1. •Transform bullet points into complete sentences with subjects, verbs, and objects
2. •Add transitions between sentences and ideas (however, moreover, in contrast, subsequently)
3. •Integrate citations naturally within sentences
4. •Expand with context and explanation that bullet points omit
5. •Ensure logical flow from one sentence to the next within each paragraph
6. •Vary sentence structure to maintain reader engagement

Semantic Matching Example

Input Section:

## 2.2 器件设计与制备

**内容要点:**
- p-MQWs-n结构的设计原理
- AlGaN外延片的外延生长
- 光刻与蒸镀电极工艺

**参考文献:**
- "High-performance AlGaN UV detector"
- "MQWs structure design for UV photodetectors"

Reference Fulltext Paragraphs:

段落1: 我们设计了一种p-MQWs-n结构的AlGaN日盲紫外探测器。首先，通过金属有机化学气相沉积（MOCVD）技术在蓝宝石衬底上生长了多层量子阱结构的外延片。

段落2: 外延片结构包括n型AlGaN层、多层量子阱有源区和p型AlGaN层。生长过程中需要严格控制温度、压强和源流量。

段落3: 制备完成后，我们采用标准的光刻工艺定义电极图案，然后通过电子束蒸镀在器件表面沉积Cr/Au电极。

Matching Result:

Output:

## 2.2 器件设计与制备

本文设计了一种p-MQWs-n（p型层-多量子阱-n型层）结构的AlGaN日盲紫外探测器[1]。该结构利用多量子阱有源区增强光电转换效率，同时通过p型和n型掺杂实现载流子的有效注入。AlGaN外延片采用金属有机化学气相沉积（MOCVD）技术在蓝宝石衬底上生长[1]。外延片结构包括n型AlGaN层、多层量子阱有源区和p型AlGaN层。生长过程中需要严格控制温度、压强和源流量，以获得高质量的晶体结构和光电特性[1]。

器件制备采用标准的光刻工艺定义电极图案，然后通过电子束蒸镀在器件表面沉积Cr/Au电极[2]。蒸镀完成后进行快速热退火处理以形成良好的欧姆接触[2]。

Output Format

Chinese Academic Paper Format

# {paper_title}

## 摘要

{concise 200-300 word summary in Chinese covering purpose, methods, results, conclusions}

**关键词:** {keyword1}; {keyword2}; {keyword3}; {keyword4}; {keyword5}

---

## 第1章 绪论

### 1.1 研究背景与意义

{full prose content with citations}

### 1.2 国内外研究现状

{full prose content with citations}

---

## 第2章 器件研究

### 2.1 引言

{full prose content with citations}

### 2.2 器件设计与制备

{full prose content with citations}

---

## 参考文献

1. {Reference 1 with full citation}
2. {Reference 2 with full citation}
...

English Journal Manuscript Format

# {paper_title}

## Abstract

{concise 100-250 word summary covering purpose, methods, results, conclusions}

**Keywords:** keyword1; keyword2; keyword3; keyword4; keyword5

## 1. Introduction

{full prose content with citations}

## 2. Related Work

{full prose content with citations}

## 3. Methods

{full prose content with procedural details}

## 4. Results

{full prose content with data presentation and statistics}

## 5. Discussion

{full prose content with interpretation, limitations, future directions}

## 6. Conclusion

{full prose content summarizing contributions}

---

## References

1. {Reference 1}
2. {Reference 2}
...

Writing Notes

**参考文献使用统计:**
- Section 2.1: [1], [2]
- Section 2.2: [1], [2]

**主要模板文献:**
- Section 2.1: "High-performance AlGaN UV detector" [1]
- Section 2.2: "High-performance AlGaN UV detector" [1]

**格式信息:**
- 语言: zh-CN
- 引文格式: APA
- 期刊格式: 标准中文学术论文

Integration

Workflow

reference-manager 输出 (需求文档解析)
    ↓
paper-writer 输入 (结构化章节 + 引用)
    ↓
遍历每个章节:
    ├── 语义匹配内容要点与文献段落
    ├── 调用 zotero_get_item_fulltext 获取全文
    ├── 以第一篇为主要模板仿写
    ├── 应用学术写作规范
    └── 添加引用
    ↓
输出完整论文

Uses Sub-Skills

• •None (standalone writing capability, integrates scientific writing principles)

Error Handling

• •No matching paragraphs found: Use abstract/metadata, warn in output
• •Insufficient references: Proceed with available sources, suggest additional references
• •Length constraint violated: Adjust content to match target length
• •Citation format error: Use fallback format (APA by default)
• •Writing blocked: Return error with suggestions
• •Missing reference fulltext: Call zotero_get_item_fulltext to fetch, report if failed

Example

Input:

{
  "paper_title": "p-MQWs-n型AlGaN日盲紫外探测器研究",
  "language": "zh-CN",
  "citation_style": "APA",
  "sections": [
    {
      "title": "第2章 器件研究",
      "subsections": [
        {
          "title": "2.1 引言",
          "content_points": ["日盲紫外探测器的重要性", "研究进展与存在的问题"],
          "references": [
            {"title": "High-performance AlGaN UV detector", "key": "ABC123"}
          ]
        }
      ]
    }
  ]
}

Output:

# p-MQWs-n型AlGaN日盲紫外探测器研究

## 摘要

本文针对日盲紫外探测应用，设计并制备了一种p-MQWs-n型AlGaN日盲紫外探测器。通过优化多量子阱结构参数，实现了高响应度和高探测率的器件性能。研究表明，该器件在254 nm波长处具有峰值响应，响应度达到... mA/W，探测率... Jones。与传统结构相比，p-MQWs-n结构具有...

**关键词:** AlGaN; 日盲紫外探测器; 多量子阱; 光电探测

---

## 第2章 器件研究

### 2.1 引言

日盲紫外探测器（波长200-280 nm）在导弹尾焰探测、臭氧层监测、医疗消毒等领域具有重要应用价值[1]。相比于可见光和红外探测器，日盲紫外探测器具有背景噪声低、定位精度高、抗干扰能力强等优势[1]。

然而，传统日盲紫外探测器面临以下挑战：响应度不足、响应速度较慢、以及稳定性有待提高等问题[1]。为解决这些问题，研究人员开展了大量关于新型结构设计的探索...

---

## 参考文献

[1] Author, A. A., & Author, B. B. (2023). High-performance AlGaN UV detector. *Journal Name*, volume(issue), pages. DOI

Common Mistakes to Avoid

• •❌ Never leave bullet points in the final manuscript
• •❌ Never use numbered or bulleted lists in Results or Discussion sections
• •❌ Don't write sentence fragments or incomplete thoughts
• •✅ Do use occasional lists only in Methods (e.g., inclusion/exclusion criteria, materials lists)
• •✅ Do ensure every section flows as connected prose
• •✅ Do read paragraphs aloud to check for natural flow
• •✅ Do define abbreviations at first use
• •✅ Do maintain consistent terminology throughout