scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

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

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+# Clinical Report Quality Assurance Checklist
+
+## General Quality Standards
+
+### Completeness
+- [ ] All required sections present
+- [ ] No blank fields or missing information
+- [ ] All relevant clinical information included
+- [ ] Timeline of events clear and complete
+- [ ] All diagnostic tests and results documented
+- [ ] All treatments and interventions documented
+- [ ] Follow-up plan specified
+
+### Accuracy
+- [ ] Patient demographics correct
+- [ ] Dates and times accurate
+- [ ] Laboratory values with correct units and reference ranges
+- [ ] Medication names, doses, and frequencies correct
+- [ ] Diagnoses coded correctly (ICD-10)
+- [ ] Procedures coded correctly (CPT if applicable)
+- [ ] No contradictory information
+
+### Clarity
+- [ ] Clear, professional language
+- [ ] Medical terminology used appropriately
+- [ ] Abbreviations defined or standard only
+- [ ] Logical organization and flow
+- [ ] Legible (if handwritten)
+- [ ] No ambiguous statements
+- [ ] Clinical reasoning clearly explained
+
+### Timeliness
+- [ ] Documented in real-time or shortly after encounter
+- [ ] Discharge summary completed within 24-48 hours
+- [ ] Critical results communicated immediately
+- [ ] Regulatory reporting deadlines met
+
+---
+
+## Case Report Quality Checklist
+
+### CARE Guidelines Compliance
+- [ ] Title includes "case report"
+- [ ] Keywords provided (2-5 MeSH terms)
+- [ ] Structured abstract with all elements
+- [ ] Introduction explains novelty
+- [ ] Patient information present and de-identified
+- [ ] Clinical findings documented
+- [ ] Timeline provided (table or figure)
+- [ ] Diagnostic assessment detailed
+- [ ] Therapeutic interventions described
+- [ ] Follow-up and outcomes reported
+- [ ] Discussion with literature review
+- [ ] Patient perspective included (if possible)
+- [ ] Informed consent statement present
+
+### Privacy and Ethics
+- [ ] Informed consent obtained and documented
+- [ ] All 18 HIPAA identifiers removed
+- [ ] Dates removed or approximated
+- [ ] Ages reported appropriately (>89 aggregated)
+- [ ] Geographic information limited to state
+- [ ] Images de-identified or consented
+- [ ] IRB approval if applicable
+
+### Scientific Quality
+- [ ] Novelty clearly established
+- [ ] Literature search comprehensive
+- [ ] Differential diagnosis considered
+- [ ] Causality addressed
+- [ ] Limitations acknowledged
+- [ ] Learning points actionable
+- [ ] References current and relevant
+
+---
+
+## Clinical Trial Report Quality Checklist
+
+### SAE Report Checklist
+- [ ] All administrative information complete
+- [ ] Subject de-identified (ID number only)
+- [ ] Event description detailed
+- [ ] MedDRA coding applied
+- [ ] Seriousness criteria documented
+- [ ] Severity assessed
+- [ ] Outcome specified
+- [ ] Causality assessment completed with rationale
+- [ ] Expectedness determined
+- [ ] Action taken with study drug documented
+- [ ] Treatment for event described
+- [ ] Narrative comprehensive and chronological
+- [ ] Critical findings communicated if applicable
+- [ ] Regulatory timelines met (7-day, 15-day)
+
+### Clinical Study Report (CSR) Checklist
+- [ ] ICH-E3 structure followed
+- [ ] Synopsis complete and accurate
+- [ ] All sections numbered correctly
+- [ ] Abbreviations defined
+- [ ] Ethics approvals documented
+- [ ] Investigator list complete
+- [ ] Study design clearly described
+- [ ] Sample size justified
+- [ ] Statistical methods specified
+- [ ] CONSORT diagram included
+- [ ] Baseline demographics table
+- [ ] Primary endpoint results
+- [ ] All secondary endpoints reported
+- [ ] Adverse events summarized
+- [ ] Individual SAE narratives included
+- [ ] Discussion and conclusions present
+- [ ] Appendices complete (protocol, CRFs, etc.)
+
+---
+
+## Diagnostic Report Quality Checklist
+
+### Radiology Report
+- [ ] Patient demographics complete
+- [ ] Clinical indication documented
+- [ ] Comparison studies noted
+- [ ] Technique described
+- [ ] Findings systematic and comprehensive
+- [ ] Measurements provided for abnormalities
+- [ ] Impression summarizes key findings
+- [ ] Answers clinical question
+- [ ] Recommendations specified
+- [ ] Critical results communicated
+- [ ] Structured reporting used if applicable (BI-RADS, Lung-RADS, etc.)
+- [ ] Report signed and dated
+
+### Pathology Report
+- [ ] Specimen labeled correctly
+- [ ] Clinical history provided
+- [ ] Gross description detailed
+- [ ] Microscopic description comprehensive
+- [ ] Diagnosis clear and specific
+- [ ] Cancer staging complete (if applicable)
+- [ ] Margins documented
+- [ ] Lymph nodes quantified
+- [ ] Synoptic reporting used for cancer (CAP protocol)
+- [ ] Immunohistochemistry results included
+- [ ] Molecular results included if applicable
+- [ ] Report signed by pathologist
+
+### Laboratory Report
+- [ ] Specimen type documented
+- [ ] Collection time documented
+- [ ] Results with units
+- [ ] Reference ranges provided
+- [ ] Critical values flagged
+- [ ] Critical values communicated
+- [ ] Specimen quality noted
+- [ ] Methodology specified (if relevant)
+- [ ] Interpretation provided (when applicable)
+- [ ] LOINC codes assigned (for interoperability)
+- [ ] Report signed and dated
+
+---
+
+## Patient Documentation Quality Checklist
+
+### SOAP Note
+- [ ] Chief complaint documented
+- [ ] HPI comprehensive (≥4 elements)
+- [ ] Review of systems performed
+- [ ] Vital signs recorded
+- [ ] Physical exam documented (relevant systems)
+- [ ] Assessment with differential diagnosis
+- [ ] Plan specific and actionable
+- [ ] Return precautions provided
+- [ ] Follow-up arranged
+- [ ] Documentation supports billing level
+- [ ] Signed, dated, and timed
+
+### History and Physical (H&P)
+- [ ] Chief complaint
+- [ ] Detailed HPI
+- [ ] Past medical history
+- [ ] Past surgical history
+- [ ] Medications reconciled
+- [ ] Allergies documented
+- [ ] Family history
+- [ ] Social history
+- [ ] Review of systems (≥10 systems for comprehensive)
+- [ ] Complete physical exam (≥8 systems)
+- [ ] Laboratory and imaging results
+- [ ] Assessment and plan for each problem
+- [ ] Code status documented
+- [ ] Completed within 24 hours of admission
+- [ ] Signed and cosigned (if required)
+
+### Discharge Summary
+- [ ] Admission and discharge dates
+- [ ] Length of stay
+- [ ] Admission diagnosis
+- [ ] Discharge diagnoses (ICD-10 coded)
+- [ ] Hospital course narrative
+- [ ] Procedures performed
+- [ ] Discharge medications reconciled
+- [ ] New/changed/discontinued medications clearly marked
+- [ ] Discharge condition
+- [ ] Discharge disposition
+- [ ] Follow-up appointments
+- [ ] Patient instructions
+- [ ] Return precautions
+- [ ] Pending tests documented
+- [ ] Code status
+- [ ] Completed within 24-48 hours
+- [ ] Sent to outpatient providers
+
+---
+
+## Regulatory Compliance Checklist
+
+### HIPAA Compliance
+- [ ] Only minimum necessary PHI disclosed
+- [ ] PHI secured and protected
+- [ ] Patient authorization obtained (if required)
+- [ ] Business associate agreement (if applicable)
+- [ ] Audit trail maintained (electronic records)
+- [ ] Breach notification procedures followed
+- [ ] De-identification performed correctly
+
+### FDA/ICH-GCP Compliance (Clinical Trials)
+- [ ] GCP principles followed
+- [ ] Informed consent documented
+- [ ] IRB approval current
+- [ ] Protocol adherence documented
+- [ ] Source documentation adequate
+- [ ] ALCOA-CCEA principles met
+- [ ] 21 CFR Part 11 compliance (electronic records)
+- [ ] Safety reporting timelines met
+- [ ] Essential documents maintained
+
+---
+
+## Writing Quality Checklist
+
+### Grammar and Style
+- [ ] Correct spelling
+- [ ] Proper grammar
+- [ ] Appropriate punctuation
+- [ ] Consistent verb tense
+- [ ] Professional tone
+- [ ] Objective language
+- [ ] No personal pronouns in formal reports
+- [ ] Active voice used appropriately
+
+### Format and Presentation
+- [ ] Consistent formatting
+- [ ] Appropriate font and size
+- [ ] Adequate margins
+- [ ] Page numbers (if applicable)
+- [ ] Headers/footers appropriate
+- [ ] Tables properly formatted with labels
+- [ ] Figures high quality with legends
+- [ ] References formatted correctly
+
+### Medical Terminology
+- [ ] Terminology accurate
+- [ ] Abbreviations standard only
+- [ ] Abbreviations defined on first use
+- [ ] Units of measurement correct
+- [ ] Drug names correct (generic preferred)
+- [ ] Anatomical terms correct
+- [ ] Coding accurate (ICD-10, CPT, MedDRA)
+
+---
+
+## Documentation Integrity Checklist
+
+### Legal and Ethical Standards
+- [ ] Facts documented, not opinions
+- [ ] Patient quotes when relevant
+- [ ] Non-compliance documented objectively
+- [ ] No alterations to original record
+- [ ] Addendums used for corrections
+- [ ] Addendums clearly labeled
+- [ ] All entries signed and dated
+- [ ] Authorship clear
+
+### Billing and Coding Support
+- [ ] Medical necessity documented
+- [ ] Complexity of care documented
+- [ ] Time documented (if time-based billing)
+- [ ] ICD-10 codes appropriate and specific
+- [ ] CPT codes match documented services
+- [ ] Modifiers appropriate
+- [ ] Documentation supports level of service billed
+
+---
+
+## Final Review Checklist
+
+Before finalizing any clinical report:
+
+- [ ] Read through entire document
+- [ ] Check for completeness
+- [ ] Verify all data accuracy
+- [ ] Ensure logical flow
+- [ ] Check spelling and grammar
+- [ ] Verify patient identifiers correct (or removed if de-identified)
+- [ ] Ensure compliance with regulations
+- [ ] Confirm all required signatures
+- [ ] Verify proper distribution
+- [ ] Archive copy appropriately
+
+---
+
+## Quality Metrics to Track
+
+- [ ] Report turnaround time
+- [ ] Amendment/addendum rate
+- [ ] Critical value communication time
+- [ ] Completeness score
+- [ ] Accuracy rate (errors per report)
+- [ ] Compliance rate
+- [ ] Patient safety events related to documentation
+- [ ] Peer review feedback
+
+---
+
+**Quality Assurance Reviewer:**
+
+**Name:** ____________________  
+**Date:** ____________________  
+**Signature:** ____________________
+
+**Quality Score:** _____ / 100
+
+**Issues Identified:**
+1. [Issue and recommendation]
+2. [Issue and recommendation]
+
+**Follow-up Required:** [ ] Yes  [ ] No
+
+

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

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+# Radiology Report Template
+
+## Patient Information
+
+**Patient Name:** [Last, First]  
+**Medical Record Number:** [MRN]  
+**Date of Birth:** [MM/DD/YYYY]  
+**Age:** [years]  
+**Sex:** [M/F]  
+**Exam Date:** [MM/DD/YYYY]  
+**Exam Time:** [HH:MM]  
+**Accession Number:** [Number]
+
+**Referring Physician:** [Name]  
+**Ordering Service:** [Service/Department]
+
+---
+
+## Examination
+
+**Exam Type:** [CT/MRI/X-Ray/Ultrasound/PET/Nuclear Medicine scan]  
+**Body Part:** [Anatomical region - e.g., Chest, Abdomen and Pelvis, Brain]  
+**Contrast:** [Yes - IV/Oral/Both | No]  
+**Laterality:** [Right/Left/Bilateral if applicable]
+
+---
+
+## Clinical Indication
+
+[Reason for examination, relevant clinical history, specific question to be answered]
+
+Example: "Rule out pulmonary embolism in patient with acute dyspnea and chest pain. History of recent surgery."
+
+---
+
+## Comparison
+
+**Prior Studies:**  
+[Modality] of [body part] from [date]: [Available/Not available for comparison]
+
+Example: "CT chest without contrast from 6 months prior (01/15/2023) available for comparison"
+
+OR: "No prior imaging available for comparison"
+
+---
+
+## Technique
+
+[Detailed description of imaging parameters and protocol]
+
+**For CT:**
+```
+Multidetector CT of the [body region] was performed [without/with] intravenous 
+contrast. [Volume] mL of [iodinated contrast agent name] was administered 
+intravenously. Images were acquired in the [arterial/venous/delayed] phase(s).
+Multiplanar reconstructions were performed.
+
+Technical quality: [Adequate / Limited by motion artifact / Limited by patient body habitus]
+Radiation dose (DLP): [mGy-cm]
+```
+
+**For MRI:**
+```
+MRI of the [body region] was performed [without/with] intravenous contrast
+using the following sequences: [list sequences - T1, T2, FLAIR, DWI, etc.]
+[Volume] mL of [gadolinium-based contrast agent] was administered intravenously.
+Multiplanar imaging was obtained.
+
+Technical quality: [Adequate / Limited by motion artifact]
+```
+
+**For X-Ray:**
+```
+[Number] views of the [body part] were obtained: [AP/PA/Lateral/Oblique]
+Technical quality: [Adequate penetration and positioning / Limited by...]
+```
+
+**For Ultrasound:**
+```
+Real-time ultrasound examination of the [body part] was performed using 
+[linear/curved] array transducer.
+Technical quality: [Adequate / Limited by bowel gas / Limited by body habitus]
+```
+
+---
+
+## Findings
+
+[Systematic, comprehensive description of findings organized by anatomical region or organ system]
+
+### [Region/Organ 1]
+
+[Detailed findings - size, density/intensity, enhancement pattern, abnormalities]
+
+**Normal statement:** "[Organ] is normal in size, contour, and [attenuation/signal intensity]. No focal lesions."
+
+**Abnormal statement:** "[Description of abnormality with measurements]"
+
+Example:
+```
+Lungs:
+- Bilateral ground-glass opacities are present, predominant in the lower lobes.
+- Right lower lobe consolidation measuring 4.5 x 3.2 cm with air bronchograms.
+- No pleural effusion or pneumothorax.
+- Airways are patent bilaterally.
+```
+
+### [Region/Organ 2]
+
+[Findings]
+
+### [Additional Regions as Applicable]
+
+**For Chest CT:**
+- Lungs
+- Airways
+- Pleura
+- Mediastinum and Hila
+- Heart and Great Vessels
+- Chest Wall
+- Upper Abdomen (if included)
+- Bones
+
+**For Abdomen/Pelvis CT:**
+- Liver
+- Gallbladder
+- Spleen
+- Pancreas
+- Kidneys and Adrenals
+- Gastrointestinal Tract
+- Peritoneum and Mesentery
+- Retroperitoneum
+- Bladder
+- Pelvic Organs
+- Vasculature
+- Lymph Nodes
+- Bones
+- Soft Tissues
+
+**For Brain MRI:**
+- Brain Parenchyma
+- Ventricles and Cisterns
+- Extra-axial Spaces
+- Vascular Structures
+- Orbits (if included)
+- Skull Base and Calvarium
+
+### Measurements (if applicable)
+
+| Structure | Measurement | Normal Range |
+|-----------|-------------|--------------|
+| [Lesion/mass] | [Size in cm, 3 dimensions] | - |
+| [Organ] | [Size] | [Normal size] |
+
+---
+
+## Impression
+
+[Concise summary of key findings with clinical interpretation]
+
+**Format as numbered list in order of clinical importance:**
+
+1. **[Most important finding]** - [Diagnosis or differential, clinical significance]
+   - [Additional details, comparison to prior if applicable]
+   - [Recommendation if any]
+
+2. **[Second finding]** - [Interpretation]
+
+3. **[Additional findings]**
+
+**Alternative format for normal study:**
+```
+No acute intrathoracic abnormality.
+Specifically, no evidence of pulmonary embolism.
+```
+
+**Recommendations (if applicable):**
+- [Further imaging, follow-up imaging interval, clinical correlation, biopsy, etc.]
+- [Timeframe for follow-up]
+
+Example:
+```
+Recommend follow-up CT in 3 months to assess for interval change.
+Clinical correlation with laboratory values recommended.
+Consider PET/CT for further characterization if clinically indicated.
+```
+
+---
+
+## Communication of Critical Results
+
+[If critical/urgent finding]
+
+**Critical finding:** [Description]
+
+**Communicated to:** [Name and role of person notified]  
+**Date/Time:** [MM/DD/YYYY at HH:MM]  
+**Method:** [Phone call / Page / In person]  
+**Read back verified:** [Yes]
+
+---
+
+## Structured Reporting (if applicable)
+
+### For Lung Nodules (Lung-RADS):
+**Category:** [Lung-RADS 0/1/2/3/4A/4B/4X]  
+**Recommendation:** [Per Lung-RADS guidelines]
+
+### For Breast Imaging (BI-RADS):
+**Category:** [BI-RADS 0/1/2/3/4/5/6]  
+**Recommendation:** [Per BI-RADS guidelines]
+
+### For Liver Lesions (LI-RADS):
+**Category:** [LI-RADS 1/2/3/4/5/M/TIV]  
+**Features:** [Arterial phase hyperenhancement, washout, capsule, size, growth]
+
+### For Prostate (PI-RADS):
+**Score:** [PI-RADS 1/2/3/4/5]  
+**Location:** [Peripheral zone / Transition zone]
+
+---
+
+## Signature
+
+**Interpreted by:**  
+[Radiologist name, MD]  
+[Board certification]  
+[NPI number if required]
+
+**Electronically signed:** [Date and time]
+
+**Dictated:** [Date and time]  
+**Transcribed:** [Date and time]  
+**Signed:** [Date and time]
+
+---
+
+## Template Notes
+
+### General Principles
+
+**Be systematic:**
+- Use consistent order (head to toe, outside to inside)
+- Don't skip regions even if normal
+- Include pertinent negatives
+
+**Be specific:**
+- Provide measurements (size in 3 dimensions for masses)
+- Describe location precisely
+- Use standardized terminology (RadLex)
+- Quantify when possible
+
+**Be clear:**
+- Avoid ambiguous language
+- Make impression stand-alone
+- Answer the clinical question directly
+- State what IS present, not just what isn't
+
+**Communication:**
+- Critical findings require immediate verbal notification
+- Document communication
+- Provide specific recommendations
+- Suggest next steps when appropriate
+
+### Measurement Guidelines
+
+**Lesions/Masses:**
+- Three dimensions: [length x width x height in cm]
+- Use consistent measurement method for follow-up
+
+**Lymph Nodes:**
+- Short axis diameter in cm
+- Note morphology (round vs. oval)
+
+**Organ Sizes:**
+- Use established normal ranges
+- Age and sex appropriate
+
+### Comparison Statements
+
+**Improved:**
+"Interval decrease in size of right upper lobe mass from 3.5 cm to 2.1 cm."
+
+**Stable:**
+"Unchanged 8 mm left lower lobe nodule, stable for 2 years."
+
+**Worsened:**
+"Interval increase in bilateral pleural effusions, now moderate on the right."
+
+**New finding:**
+"New 1.5 cm right adrenal nodule, not present on prior CT."
+
+### Differential Diagnosis Language
+
+**Definite:** "Consistent with..."  
+**Probable:** "Most likely represents..." or "Favors..."  
+**Possible:** "Suggestive of..." or "Differential diagnosis includes..."  
+**Uncertain:** "Cannot exclude..." or "Consider..."
+
+### Recommendations
+
+**Follow-up imaging:**
+- Specify modality, timing, and what to assess
+- "Recommend CT chest in 6-12 months to assess stability"
+
+**Further characterization:**
+- "Consider MRI for further characterization"
+- "Ultrasound correlation recommended"
+
+**Clinical correlation:**
+- "Clinical correlation with tumor markers recommended"
+- "Correlate with patient symptoms and physical examination"
+
+**Biopsy/Intervention:**
+- "Consider biopsy for definitive diagnosis"
+- "Amenable to image-guided biopsy if clinically indicated"
+
+