scientific-writer 2.2.1__py3-none-any.whl → 2.2.3__py3-none-any.whl

scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md

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+# Clinical Case Report Template
+
+## Title
+
+[Insert descriptive title that includes "Case Report" or "Case Study" and indicates the clinical focus]
+
+Example: Unusual Presentation of Acute Appendicitis in an Elderly Patient: A Case Report
+
+## Author Information
+
+[Author names, affiliations, ORCID IDs]
+
+**Corresponding Author:**  
+[Name]  
+[Email]  
+[Institution]
+
+## Keywords
+
+[2-5 keywords, preferably MeSH terms]
+
+Example: Appendicitis, Atypical presentation, Elderly, Diagnostic imaging
+
+## Abstract
+
+### Introduction
+[What is unique about this case? Why is it worth reporting? 1-2 sentences]
+
+### Patient Concerns
+[Primary symptoms and chief complaint]
+
+### Diagnosis
+[Final diagnosis, how it was reached]
+
+### Interventions
+[Key treatments provided]
+
+### Outcomes
+[Clinical outcome and follow-up status]
+
+### Lessons
+[Main takeaway messages for clinicians]
+
+**Word count:** [150-250 words]
+
+## Introduction
+
+[Background information - 2-4 paragraphs]
+
+**Paragraph 1:** Background on the condition
+- Epidemiology of the condition
+- Typical clinical presentation
+- Standard diagnostic approach
+- Current treatment guidelines
+
+**Paragraph 2:** Why this case is novel
+- What makes this case unusual or important
+- Gap in medical knowledge addressed
+- Literature review showing rarity or uniqueness
+- Clinical significance
+
+**Paragraph 3:** Objectives
+- Purpose of reporting this case
+- Learning points to be highlighted
+
+## Patient Information
+
+**Demographics:**
+- Age: [e.g., "A 72-year-old" or "A woman in her 70s"]
+- Sex: [Male/Female]
+- Ethnicity: [if relevant to case]
+- Occupation: [if relevant]
+
+**Medical History:**
+- Past medical history: [chronic conditions]
+- Past surgical history: [prior surgeries]
+- Family history: [relevant family history]
+- Social history: [tobacco, alcohol, occupation, living situation]
+
+**Medications:**
+- Current medications: [list with doses]
+- Allergies: [drug allergies and reactions]
+
+**Presenting Symptoms:**
+- Chief complaint: ["Patient's words" or clinical presentation]
+- Duration of symptoms
+- Severity and characteristics
+- Associated symptoms
+- Relevant review of systems
+
+## Clinical Findings
+
+**Physical Examination:**
+- Vital signs: [T, BP, HR, RR, SpO2]
+- General appearance: [overall state]
+- Systematic examination by organ system:
+  - HEENT: [findings]
+  - Cardiovascular: [findings]
+  - Respiratory: [findings]
+  - Abdomen: [findings]
+  - Neurological: [findings]
+  - Other relevant systems: [findings]
+
+**Pertinent Negatives:**
+[Important negative findings]
+
+## Timeline
+
+| Date/Time | Event |
+|-----------|-------|
+| [Day -X or Date] | [Initial symptom onset] |
+| [Day 0 or Date] | [Presentation to healthcare] |
+| [Day 0 or Date] | [Initial evaluation and tests] |
+| [Day X or Date] | [Diagnosis confirmed] |
+| [Day X or Date] | [Treatment initiated] |
+| [Day X or Date] | [Hospital discharge or follow-up] |
+| [Month X or Date] | [Long-term follow-up] |
+
+*Note: Use relative days (Day 0, Day 1) or approximate dates (Month 1, Month 3) to protect patient privacy*
+
+## Diagnostic Assessment
+
+### Initial Diagnostic Workup
+
+**Laboratory Tests:**
+| Test | Result | Reference Range | Interpretation |
+|------|--------|----------------|----------------|
+| [Test name] | [Value with units] | [Normal range] | [High/Low/Normal] |
+
+**Imaging Studies:**
+- [Modality] ([Date]): [Key findings]
+- [Include images if applicable, with labels and arrows pointing to key findings]
+
+**Other Diagnostic Procedures:**
+- [Procedure name] ([Date]): [Findings]
+
+### Differential Diagnosis
+
+**Diagnoses Considered:**
+1. [Primary differential]
+   - Supporting evidence:
+   - Evidence against:
+2. [Alternative diagnosis]
+   - Supporting evidence:
+   - Evidence against:
+3. [Additional differentials as appropriate]
+
+### Diagnostic Challenges
+
+[Describe any difficulties in reaching the diagnosis]
+- Atypical presentation
+- Misleading initial findings
+- Diagnostic delays
+- Complex decision-making
+
+### Final Diagnosis
+
+**Confirmed Diagnosis:** [Final diagnosis with ICD-10 code if applicable]
+
+**Diagnostic Reasoning:**
+[Explain how diagnosis was reached, key diagnostic features, confirmatory tests]
+
+## Therapeutic Intervention
+
+### Treatment Approach
+
+**Initial Management:**
+- [Immediate interventions]
+- [Supportive care]
+- [Monitoring]
+
+**Definitive Treatment:**
+1. **Pharmacological Interventions:**
+   - [Drug name]: [Dose, route, frequency, duration]
+   - Indication: [Why prescribed]
+   - Response: [Patient response to treatment]
+
+2. **Procedural/Surgical Interventions:**
+   - [Procedure name] performed on [date/day]
+   - Indication: [Why performed]
+   - Technique: [Brief description]
+   - Findings: [Intraoperative or procedural findings]
+   - Complications: [Any complications or none]
+
+3. **Other Interventions:**
+   - [Physical therapy, dietary modifications, etc.]
+
+**Alternative Treatments Considered:**
+[Other treatment options that were considered and why they were not pursued]
+
+**Changes to Interventions:**
+[Any modifications to treatment plan]
+- Date of change:
+- Reason for change:
+- New intervention:
+
+## Follow-up and Outcomes
+
+**Immediate Outcome:**
+[Outcome during hospitalization or initial treatment period]
+- Clinical response:
+- Laboratory or imaging follow-up:
+- Complications:
+- Length of hospitalization (if applicable):
+
+**Short-term Follow-up:** ([Timeframe, e.g., 1 month])
+- Clinical status:
+- Follow-up tests:
+- Adherence to treatment:
+- Any issues or concerns:
+
+**Long-term Follow-up:** ([Timeframe, e.g., 6 months, 1 year])
+- Clinical status:
+- Recovery or resolution:
+- Functional status:
+- Quality of life:
+- Recurrence or complications:
+
+**Patient-Reported Outcomes:**
+[Symptoms, quality of life, patient satisfaction]
+
+## Discussion
+
+**Paragraph 1: Summary and Significance**
+[Briefly summarize the case and state its significance]
+
+**Paragraph 2: Literature Review**
+[Review similar cases in the literature]
+- Number of similar cases reported
+- Comparison to this case
+- What is novel about this case
+- [Cite relevant references]
+
+**Paragraph 3: Clinical Implications**
+[What can clinicians learn from this case?]
+- Recognition of atypical presentations
+- Diagnostic pearls
+- Treatment considerations
+- When to consider this diagnosis
+
+**Paragraph 4: Pathophysiology or Mechanism (if applicable)**
+[Explain underlying mechanism, why this occurred, contributing factors]
+
+**Paragraph 5: Strengths and Limitations**
+[Acknowledge limitations of case report]
+- Single case report limitations
+- Cannot establish causation
+- Generalizability concerns
+- Strengths of comprehensive evaluation
+
+**Paragraph 6: Future Directions**
+[Unanswered questions, areas for future research]
+
+## Learning Points
+
+- [Point 1: Concise, actionable clinical lesson]
+- [Point 2: Key diagnostic or treatment pearl]
+- [Point 3: When to consider this diagnosis]
+- [Point 4: (optional) Additional takeaway]
+
+## Patient Perspective
+
+[Optional but encouraged: Patient's own description of experience, in their own words if possible]
+
+"[Patient quote describing their experience, symptoms, treatment, or outcome]"
+
+[Or narrative description of patient's perspective, impact on quality of life, satisfaction with care]
+
+## Informed Consent
+
+Written informed consent was obtained from the patient for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal on request.
+
+[OR if patient deceased/unable to consent:]
+
+Written informed consent was obtained from the patient's next of kin for publication of this case report, as the patient was deceased [or unable to provide consent due to...] at the time of manuscript preparation.
+
+## Conflicts of Interest
+
+The authors declare that they have no conflicts of interest.
+
+## Funding
+
+This case report received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.
+
+[OR: This work was supported by [funding source and grant number]]
+
+## Acknowledgments
+
+[Acknowledge contributors who do not meet authorship criteria, providers who cared for patient, etc.]
+
+## References
+
+[Format according to journal requirements - typically AMA, Vancouver, or APA]
+
+1. [First reference - Author(s). Title. Journal. Year;Volume(Issue):Pages.]
+2. [Second reference...]
+
+---
+
+## CARE Checklist Completion
+
+Use the CARE checklist to ensure all required elements are included:
+
+- [ ] Title includes "case report"
+- [ ] Keywords provided (2-5)
+- [ ] Structured/unstructured abstract
+- [ ] Introduction with background and novelty
+- [ ] Patient demographics (de-identified)
+- [ ] Clinical findings
+- [ ] Timeline
+- [ ] Diagnostic assessment
+- [ ] Therapeutic interventions
+- [ ] Follow-up and outcomes
+- [ ] Discussion with literature review
+- [ ] Patient perspective (if possible)
+- [ ] Informed consent statement
+- [ ] All 18 HIPAA identifiers removed
+- [ ] References formatted correctly
+- [ ] Figures/tables labeled and referenced
+- [ ] Word count within journal limits
+
+---
+
+## De-identification Checklist
+
+Verify all HIPAA identifiers removed:
+
+- [ ] Names (patient, family, providers)
+- [ ] Geographic locations smaller than state
+- [ ] Exact dates (use year only or relative time)
+- [ ] Phone numbers
+- [ ] Email addresses
+- [ ] Medical record numbers
+- [ ] Account numbers
+- [ ] License numbers
+- [ ] Device serial numbers
+- [ ] URLs
+- [ ] IP addresses
+- [ ] Biometric identifiers
+- [ ] Full-face photos (cropped or blurred)
+- [ ] Any other identifying information
+
+---
+
+**Notes:**
+- Adapt this template to your specific journal's requirements
+- Check word count limits (typically 1500-3000 words)
+- Follow journal's reference style
+- Include institutional review/ethics exemption if applicable
+- Consider attaching CARE checklist when submitting
+
+

scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md

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+# Clinical Study Report (CSR) Template
+## ICH-E3 Format
+
+---
+
+# TITLE PAGE
+
+**Study Title:** [Full descriptive title including compound, indication, phase]
+
+**Protocol Number:** [Sponsor protocol number]  
+**Protocol Version:** [Final protocol version and date]
+
+**Sponsor:** [Company name and address]  
+**Compound/Drug Name:** [Generic and proprietary names, compound code]  
+**Indication:** [Therapeutic area and specific indication studied]
+
+**Study Phase:** [I / II / III / IV]  
+**Study Type:** [Interventional / Observational]
+
+**Report Date:** [MM/DD/YYYY]  
+**Report Version:** [Version number]
+
+**Medical Expert:** [Name, MD, Title]  
+**Biostatistician:** [Name, PhD, Title]
+
+**Confidentiality Statement:**
+"This document contains confidential information belonging to [Sponsor]. It may not be reproduced or distributed without permission."
+
+---
+
+# SYNOPSIS
+
+**Title:** [Abbreviated title]
+
+**Protocol Number:** [Number]  
+**Study Phase:** [Phase]  
+**Study Period:** [Start date - End date]
+
+## Study Objectives
+
+**Primary Objective:**
+[State primary objective clearly and concisely]
+
+**Secondary Objectives:**
+- [Secondary objective 1]
+- [Secondary objective 2]
+
+## Methodology
+
+**Study Design:**
+[Randomized, double-blind, placebo-controlled, parallel-group, etc.]
+
+**Study Population:**
+- Target population: [Patient population]
+- Key inclusion criteria: [Main criteria]
+- Key exclusion criteria: [Main criteria]
+
+**Sample Size:**
+- Planned: [N participants]
+- Randomized: [N participants]
+- Completed: [N participants]
+
+**Treatment:**
+- Treatment A: [Drug name, dose, route, frequency]
+- Treatment B: [Comparator/placebo]
+- Treatment duration: [Weeks/months]
+- Follow-up duration: [Weeks/months]
+
+**Endpoints:**
+
+Primary:
+- [Primary endpoint definition and timepoint]
+
+Secondary:
+- [Secondary endpoint 1]
+- [Secondary endpoint 2]
+
+**Statistical Methods:**
+[Brief description of analysis approach, significance level, handling of multiplicity]
+
+## Results
+
+**Participant Disposition:**
+- Screened: [N]
+- Randomized: [N Treatment A, N Treatment B]
+- Completed: [N Treatment A, N Treatment B]
+- Discontinued: [N overall, % - main reasons]
+
+**Demographics and Baseline:**
+[Summary of key baseline characteristics, comparability across groups]
+
+**Efficacy Results:**
+
+Primary Endpoint:
+- [Result for Treatment A vs B, effect size, 95% CI, p-value]
+
+Secondary Endpoints:
+- [Results for each secondary endpoint]
+
+**Safety Results:**
+- Any AE: [% Treatment A vs B]
+- Treatment-related AE: [% Treatment A vs B]
+- Serious AE: [% Treatment A vs B]
+- Discontinuations due to AE: [% Treatment A vs B]
+- Deaths: [N Treatment A vs B]
+- Common AEs (≥5%): [List with percentages]
+
+## Conclusions
+
+[Overall conclusions regarding efficacy and safety, benefit-risk assessment]
+
+---
+
+# TABLE OF CONTENTS
+
+[Detailed table of contents with page numbers]
+
+---
+
+# LIST OF ABBREVIATIONS
+
+| Abbreviation | Definition |
+|--------------|------------|
+| AE | Adverse Event |
+| ANCOVA | Analysis of Covariance |
+| CI | Confidence Interval |
+| CSR | Clinical Study Report |
+| FAS | Full Analysis Set |
+| GCP | Good Clinical Practice |
+| ICF | Informed Consent Form |
+| ITT | Intent-to-Treat |
+| PP | Per-Protocol |
+| SAE | Serious Adverse Event |
+| SD | Standard Deviation |
+| [Add study-specific abbreviations] | |
+
+---
+
+# ETHICS (Section 2)
+
+## 2.1 Independent Ethics Committee (IEC) or Institutional Review Board (IRB)
+
+[List of all IECs/IRBs that approved the study]
+
+| Site Number | Institution | IRB/IEC Name | Approval Date |
+|-------------|------------|--------------|---------------|
+| 001 | [Institution] | [IRB name] | [MM/DD/YYYY] |
+
+## 2.2 Ethical Conduct of the Study
+
+This study was conducted in accordance with:
+- ICH Good Clinical Practice (GCP) E6(R2)
+- Declaration of Helsinki (current version)
+- Applicable regulatory requirements
+- Sponsor Standard Operating Procedures
+
+## 2.3 Patient Information and Consent
+
+Informed consent was obtained from all participants before any study-specific procedures. The informed consent process included:
+- Written information about study purpose, procedures, risks, and benefits
+- Opportunity to ask questions
+- Voluntary participation with right to withdraw
+- Signatures of participant and person obtaining consent
+- Copy provided to participant
+
+---
+
+# INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE (Section 3)
+
+## 3.1 Investigators and Study Centers
+
+[Table listing all investigators, sites, and enrollment]
+
+| Site No. | Investigator | Institution | City, Country | Subjects Enrolled |
+|----------|--------------|-------------|---------------|-------------------|
+| 001 | [Name, MD] | [Institution] | [City, Country] | [N] |
+
+**Coordinating Investigator:** [Name, if applicable]
+
+## 3.2 Study Administrative Structure
+
+**Sponsor:**
+- Medical Monitor: [Name, credentials]
+- Project Manager: [Name]
+- Biostatistician: [Name, credentials]
+
+**Contract Research Organization (CRO):** [Name, if applicable]
+- [Responsibilities]
+
+## 3.3 Responsibilities of Parties Involved
+
+[Description of sponsor, investigator, CRO, DSMB responsibilities]
+
+---
+
+# INTRODUCTION (Section 4)
+
+## 4.1 Background
+
+[Detailed background on disease/condition, unmet medical need, treatment landscape]
+
+## 4.2 Nonclinical Studies
+
+[Summary of relevant preclinical pharmacology, toxicology, and safety findings]
+
+## 4.3 Previous Clinical Studies
+
+[Summary of prior clinical experience with investigational product]
+
+## 4.4 Study Rationale and Objectives
+
+[Justification for conducting this study, specific objectives]
+
+---
+
+# STUDY OBJECTIVES AND PLAN (Section 5)
+
+## 5.1 Objectives and Endpoints
+
+**Primary Objective:**
+[Objective statement]
+
+**Primary Endpoint:**
+[Detailed endpoint definition, measurement method, timepoint]
+
+**Secondary Objectives:**
+1. [Objective]
+2. [Objective]
+
+**Secondary Endpoints:**
+1. [Endpoint definition]
+2. [Endpoint definition]
+
+## 5.2 Study Design
+
+[Detailed description of study design with diagram if helpful]
+
+**Design Type:** [Parallel, crossover, factorial, etc.]
+**Blinding:** [Double-blind, open-label, etc.]
+**Randomization:** [1:1, 2:1, stratified, etc.]
+**Duration:** [Treatment period, follow-up period]
+
+**Study Schema:**
+[Flow diagram showing screening, randomization, treatment periods, follow-up]
+
+## 5.3 Study Population
+
+**Key Inclusion Criteria:**
+1. [Criterion]
+2. [Criterion]
+
+**Key Exclusion Criteria:**
+1. [Criterion]
+2. [Criterion]
+
+## 5.4 Treatments
+
+**Investigational Product:**
+- Name: [Generic, trade, code]
+- Formulation: [Tablet, capsule, injection]
+- Dose: [Dose and regimen]
+- Route: [PO, IV, SC, etc.]
+- Packaging and labeling: [Description]
+
+**Comparator:**
+[Similar details for comparator or placebo]
+
+**Concomitant Medications:**
+[Permitted and prohibited medications]
+
+## 5.5 Sample Size Determination
+
+**Target Sample Size:** [N per group, N total]
+
+**Justification:**
+- Assumed effect size: [Value]
+- Variability (SD): [Value]
+- Type I error (α): [0.05]
+- Power (1-β): [80% or 90%]
+- Expected dropout rate: [%]
+- Two-sided test
+
+## 5.6 Statistical Analysis Plan
+
+**Analysis Populations:**
+- Full Analysis Set (FAS): [Definition]
+- Per-Protocol Set (PPS): [Definition]
+- Safety Analysis Set: [Definition]
+
+**Statistical Methods:**
+- Primary endpoint: [Method - e.g., ANCOVA with baseline as covariate]
+- Secondary endpoints: [Methods]
+- Handling of missing data: [Approach]
+- Multiplicity adjustment: [Method if applicable]
+- Interim analyses: [If planned]
+
+**Significance Level:** α = 0.05 (two-sided)
+
+---
+
+# STUDY PATIENTS (Section 6)
+
+## 6.1 Disposition of Patients
+
+**Participant Flow (CONSORT Diagram):**
+
+[Include detailed CONSORT diagram showing screening through analysis]
+
+**Summary Table:**
+
+| Category | Treatment A | Treatment B | Total |
+|----------|-------------|-------------|-------|
+| Screened | N | N | N |
+| Screen failures | N (%) | N (%) | N (%) |
+| Randomized | N | N | N |
+| Received treatment | N (%) | N (%) | N (%) |
+| Completed | N (%) | N (%) | N (%) |
+| Discontinued | N (%) | N (%) | N (%) |
+| - Adverse event | N (%) | N (%) | N (%) |
+| - Lack of efficacy | N (%) | N (%) | N (%) |
+| - Lost to follow-up | N (%) | N (%) | N (%) |
+| - Withdrawal of consent | N (%) | N (%) | N (%) |
+| - Other | N (%) | N (%) | N (%) |
+
+## 6.2 Protocol Deviations
+
+**Major Protocol Deviations:**
+[Summary of major deviations, impact on data, subjects affected]
+
+**Important Protocol Deviations by Category:**
+
+| Deviation Type | Treatment A | Treatment B | Total |
+|----------------|-------------|-------------|-------|
+| Inclusion/exclusion criteria | N (%) | N (%) | N (%) |
+| Dosing errors | N (%) | N (%) | N (%) |
+| Prohibited medications | N (%) | N (%) | N (%) |
+| Missed visits | N (%) | N (%) | N (%) |
+
+---
+
+(Continues with sections 7-14 following ICH-E3 structure...)
+
+---
+
+**Note:** This is an abbreviated template. A complete CSR following ICH-E3 is typically 50-300 pages with extensive appendices. Key sections to complete:
+- Section 7: Efficacy Evaluation
+- Section 8: Safety Evaluation
+- Section 9: Discussion and Overall Conclusions
+- Section 10: Tables, Figures, and Graphs
+- Section 11: References
+- Section 12-14: Appendices (Protocol, CRFs, Investigator list, etc.)
+
+