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

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

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+# Serious Adverse Event (SAE) Report Template
+
+## Report Information
+
+**Report Type:** [ ] Initial Report  [ ] Follow-up Report  [ ] Final Report  
+**Report Number:** [SAE-YYYY-####]  
+**Report Date:** [MM/DD/YYYY]  
+**Reporter:** [Name and title]  
+**Reporter Contact:** [Email and phone]
+
+**Follow-up Number:** [If follow-up: #1, #2, etc.]  
+**Previous Report Date:** [If follow-up]
+
+---
+
+## Study Information
+
+**Protocol Number:** [Protocol ID]  
+**Protocol Title:** [Full study title]  
+**Study Phase:** [ ] Phase I  [ ] Phase II  [ ] Phase III  [ ] Phase IV  
+**Study Sponsor:** [Sponsor name]  
+**IND/IDE Number:** [IND or IDE number if applicable]  
+**ClinicalTrials.gov ID:** [NCT number]
+
+**Principal Investigator:** [Name]  
+**Site Number:** [Site ID]  
+**Site Name:** [Institution name]
+
+---
+
+## Subject Information (De-identified)
+
+**Subject ID / Randomization Number:** [ID only, no name]  
+**Subject Initials:** [XX] (if permitted by regulatory authority)  
+**Age:** [Years] OR **Date of Birth:** [Year only: YYYY]  
+**Sex:** [ ] Male  [ ] Female  [ ] Other  
+**Race:** [Category]  
+**Ethnicity:** [Hispanic or Latino / Not Hispanic or Latino]  
+**Weight:** [kg]  
+**Height:** [cm]
+
+**Study Arm / Treatment Group:** [ ] Treatment A  [ ] Treatment B  [ ] Placebo  [ ] Blinded
+
+**Date of Informed Consent:** [MM/DD/YYYY]  
+**Date of First Study Drug:** [MM/DD/YYYY]  
+**Date of Last Study Drug:** [MM/DD/YYYY]  
+**Study Drug Status at Time of Event:** [ ] Ongoing  [ ] Completed  [ ] Discontinued
+
+---
+
+## Adverse Event Information
+
+**Reported Term (Verbatim):** [Exact term reported by investigator/patient]
+
+**MedDRA Coding:**
+- **Preferred Term (PT):** [MedDRA PT]
+- **System Organ Class (SOC):** [MedDRA SOC]
+- **MedDRA Version:** [e.g., 25.0]
+
+**Event Description:**
+[Detailed narrative description of the adverse event]
+
+**Date of Onset:** [MM/DD/YYYY]  
+**Time of Onset:** [HH:MM] (if known and relevant)  
+**Date of Resolution:** [MM/DD/YYYY] OR [ ] Ongoing  
+**Duration:** [Days/hours if resolved]
+
+**Event Location:** [ ] Inpatient  [ ] Outpatient  [ ] Home  [ ] Other: ________
+
+---
+
+## Seriousness Criteria
+
+**This event is considered serious because it resulted in or required:**
+
+- [ ] **Death** - Date of death: [MM/DD/YYYY]
+- [ ] **Life-threatening** - Immediate risk of death at time of event
+- [ ] **Hospitalization (initial or prolonged)** - Dates: [MM/DD/YYYY to MM/DD/YYYY]
+- [ ] **Persistent or significant disability/incapacity**
+- [ ] **Congenital anomaly/birth defect**
+- [ ] **Medically important event** - Explanation: _________________
+
+**Hospitalization Details (if applicable):**
+- Admission Date: [MM/DD/YYYY]
+- Discharge Date: [MM/DD/YYYY] OR [ ] Still hospitalized
+- Hospital Name: [Name and location]
+- ICU Admission: [ ] Yes  [ ] No  
+  - If yes, dates: [MM/DD/YYYY to MM/DD/YYYY]
+
+---
+
+## Severity Assessment
+
+**Severity (Intensity):**
+- [ ] **Mild** - Noticeable but does not interfere with daily activities
+- [ ] **Moderate** - Interferes with daily activities but manageable
+- [ ] **Severe** - Prevents usual daily activities, requires intervention
+
+*Note: Severity is not the same as seriousness*
+
+---
+
+## Outcome
+
+- [ ] **Recovered/Resolved** - Complete resolution, returned to baseline
+- [ ] **Recovering/Resolving** - Improving but not yet fully resolved
+- [ ] **Not Recovered/Not Resolved** - Ongoing without improvement
+- [ ] **Recovered/Resolved with Sequelae** - Persistent effects remain
+- [ ] **Fatal** - Event resulted in death
+- [ ] **Unknown** - Unable to determine outcome
+
+**Date of Final Outcome (if resolved):** [MM/DD/YYYY]
+
+---
+
+## Causality Assessment
+
+**Relationship to Study Drug:**
+- [ ] **Not Related** - Clearly due to other cause
+- [ ] **Unlikely Related** - Doubtful connection to study drug
+- [ ] **Possibly Related** - Could be related, but other causes possible
+- [ ] **Probably Related** - More likely related to study drug than other causes
+- [ ] **Definitely Related** - Certain relationship to study drug
+
+**Relationship to Study Procedures:**
+- [ ] Not Related  [ ] Unlikely  [ ] Possibly  [ ] Probably  [ ] Definitely
+
+**Relationship to Underlying Disease:**
+- [ ] Not Related  [ ] Unlikely  [ ] Possibly  [ ] Probably  [ ] Definitely
+
+**Relationship to Concomitant Medications:**
+- [ ] Not Related  [ ] Unlikely  [ ] Possibly  [ ] Probably  [ ] Definitely
+- Suspected medication(s): _____________________
+
+**Rationale for Causality Assessment:**
+[Detailed explanation of causality determination, including temporal relationship, biological plausibility, dechallenge/rechallenge if applicable, alternative explanations]
+
+---
+
+## Expectedness
+
+**Is this event expected based on the Investigator's Brochure or protocol?**
+- [ ] **Expected** - Listed in IB/protocol with similar characteristics
+- [ ] **Unexpected** - Not listed OR more severe than documented
+
+**Reference:** [IB version and section, or protocol section]
+
+---
+
+## Action Taken with Study Drug
+
+- [ ] **No change** - Study drug continued at same dose
+- [ ] **Dose reduced** - New dose: ______ (from ______)
+- [ ] **Dose increased** - New dose: ______ (from ______)
+- [ ] **Drug interrupted** - Dates: [MM/DD to MM/DD]
+  - [ ] Resumed  [ ] Not resumed
+- [ ] **Drug permanently discontinued** - Date: [MM/DD/YYYY]
+- [ ] **Not applicable** - Event occurred after study drug discontinued
+
+**Dechallenge:** [ ] Positive (improved after stopping)  [ ] Negative  [ ] Not done
+
+**Rechallenge:** [ ] Positive (recurred after restarting)  [ ] Negative  [ ] Not done
+
+---
+
+## Treatment and Interventions
+
+**Treatments Given for This Event:**
+
+1. **[Medication/Procedure]**
+   - Dose/Details: _________________
+   - Route: _________________
+   - Start Date: [MM/DD/YYYY]
+   - Stop Date: [MM/DD/YYYY] OR [ ] Ongoing
+   - Response: [ ] Effective  [ ] Partially effective  [ ] Not effective
+
+2. **[Additional treatments]**
+
+**Hospitalization Interventions:**
+- [ ] IV fluids
+- [ ] Oxygen therapy
+- [ ] Mechanical ventilation
+- [ ] Surgical intervention - Procedure: ______________
+- [ ] ICU care
+- [ ] Other: ______________
+
+---
+
+## Relevant Medical History
+
+**Pre-existing Conditions Relevant to This Event:**
+[List conditions that may be related to the event]
+
+**Concomitant Medications at Time of Event:**
+
+| Medication | Indication | Dose/Frequency | Start Date | Stop Date |
+|------------|-----------|----------------|------------|-----------|
+| [Name] | [Indication] | [Dose] | [MM/DD/YYYY] | [MM/DD/YYYY or Ongoing] |
+
+---
+
+## Laboratory and Diagnostic Tests
+
+**Relevant Laboratory Values:**
+
+| Test | Result | Units | Reference Range | Date | Relation to Event |
+|------|--------|-------|----------------|------|-------------------|
+| [Test] | [Value] | [Units] | [Range] | [MM/DD] | [Before/During/After] |
+
+**Imaging/Diagnostic Studies:**
+- **[Study type] ([Date]):** [Key findings]
+
+**ECG/Monitoring:**
+[Results if relevant]
+
+---
+
+## Detailed Event Narrative
+
+[Comprehensive chronological narrative of the event]
+
+**Minimum elements to include:**
+- Patient demographics and study participation timeline
+- Relevant medical history
+- Chronological description of event development
+- Symptoms, signs, and clinical course
+- Diagnostic workup and results
+- Treatments administered and response
+- Clinical outcome and current status
+- Investigator's assessment of causality and reasoning
+
+**Example Structure:**
+```
+A [age]-year-old [sex] with a history of [relevant medical conditions] enrolled in 
+Study [protocol] on [date] and was randomized to [treatment arm]. The patient had 
+been receiving [study drug] at [dose] for [duration] when, on [date], the patient 
+developed [initial symptoms]. 
+
+[Describe progression of symptoms, timeline, clinical findings...]
+
+[Describe diagnostic workup performed and results...]
+
+[Describe treatments given and patient response...]
+
+[Describe outcome and current status...]
+
+The investigator assessed this event as [causality] related to study drug because 
+[reasoning]. Alternative explanations include [list alternative causes considered].
+```
+
+---
+
+## Investigator Assessment
+
+**Investigator's Comments:**
+[Additional relevant information, clinical interpretation, conclusions]
+
+**Does this event meet criteria for expedited reporting to regulatory authorities?**
+- [ ] Yes - Fatal or life-threatening unexpected SAE
+- [ ] Yes - Other unexpected SAE
+- [ ] No - Expected event
+
+---
+
+## Follow-up Information Required
+
+**Information Pending (if initial or follow-up report):**
+- [ ] Final outcome
+- [ ] Laboratory results
+- [ ] Pathology report
+- [ ] Imaging results
+- [ ] Autopsy results (if death)
+- [ ] Consultant reports
+- [ ] Medical records
+- [ ] Dechallenge/rechallenge information
+- [ ] Other: ______________
+
+**Expected Date for Follow-up Report:** [MM/DD/YYYY]
+
+---
+
+## Regulatory Reporting
+
+**Sponsor Safety Assessment:**
+[To be completed by sponsor]
+- Expectedness: [ ] Expected  [ ] Unexpected
+- Relationship: [ ] Related  [ ] Not related
+- Reportable to FDA/EMA: [ ] Yes  [ ] No
+- Timeline: [ ] 7-day  [ ] 15-day  [ ] Annual
+
+**IRB Notification:**
+- Reported to IRB: [ ] Yes  [ ] No  [ ] Not required
+- Date reported: [MM/DD/YYYY]
+- IRB determination: _______________
+
+---
+
+## Signatures
+
+**Investigator Signature:**
+
+**Name:** [Principal Investigator name]  
+**Title:** [MD, credentials]  
+**Signature:** ____________________  
+**Date:** [MM/DD/YYYY]
+
+**I certify that this report is accurate and complete to the best of my knowledge.**
+
+---
+
+**Sponsor Representative (if applicable):**
+
+**Name:** [Name]  
+**Title:** [Medical Monitor, Safety Officer]  
+**Signature:** ____________________  
+**Date:** [MM/DD/YYYY]
+
+---
+
+## Attachments
+
+- [ ] Relevant laboratory reports
+- [ ] Imaging reports
+- [ ] Pathology reports
+- [ ] Discharge summary
+- [ ] Death certificate (if applicable)
+- [ ] Autopsy report (if applicable)
+- [ ] Consultant notes
+- [ ] Other: ______________
+
+---
+
+## Distribution List
+
+- [ ] Study Sponsor
+- [ ] FDA (if applicable)
+- [ ] IRB/IEC
+- [ ] Data Safety Monitoring Board (if applicable)
+- [ ] Site regulatory files
+
+---
+
+## Notes
+
+**Regulatory Timeline Requirements:**
+- **Fatal or life-threatening unexpected SAEs:** 7 days for preliminary report, 15 days for complete
+- **Other serious unexpected events:** 15 days
+- **IRB notification:** Per institutional policy (typically 5-10 days)
+
+**Key Points:**
+- Complete all sections accurately
+- Provide detailed narrative
+- Include temporal relationships
+- Document all sources of information
+- Follow up until event resolved
+- Maintain patient confidentiality
+- Use only de-identified information
+
+

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

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+# Consultation Note Template
+
+**Patient Name:** [Last, First]  
+**Medical Record Number:** [MRN]  
+**Date of Birth:** [MM/DD/YYYY]  
+**Age/Sex:** [years, M/F]
+
+**Consultation Date:** [MM/DD/YYYY]  
+**Consultation Time:** [HH:MM]  
+**Location:** [Floor, Room number]
+
+**Requesting Service:** [Primary team]  
+**Requesting Physician:** [Name]  
+**Consulting Service:** [Cardiology, Nephrology, etc.]  
+**Consulting Physician:** [Name and credentials]
+
+---
+
+## Reason for Consultation
+
+[Specific clinical question or reason for consultation]
+
+Example: "Please evaluate and manage acute kidney injury in setting of heart failure exacerbation."
+
+---
+
+## History of Present Illness (Focused on Consultation Question)
+
+[Relevant history focused on the consultation question]
+
+[Patient Name] is a [age]-year-old [sex] with a history of [relevant conditions] currently admitted to [service] for [admission diagnosis] who is being consulted for [specific issue].
+
+[Chronological narrative relevant to consultation question]
+
+**Timeline of Current Issue:**
+- [Key events leading to consultation]
+- [Current status]
+- [Treatments tried]
+
+---
+
+## Relevant Past Medical History
+
+1. [Condition relevant to consultation]
+2. [Additional relevant conditions]
+
+[Only include history pertinent to consultation question]
+
+---
+
+## Current Medications
+
+[List medications relevant to consultation question]
+
+| Medication | Dose | Route | Frequency | Relevant to: |
+|------------|------|-------|-----------|--------------|
+| [Drug] | [mg] | [route] | [freq] | [Why relevant] |
+
+---
+
+## Allergies
+
+| Allergen | Reaction |
+|----------|----------|
+| [Drug/substance] | [Reaction] |
+
+---
+
+## Relevant Social/Family History
+
+[Only include if pertinent to consultation]
+
+---
+
+## Review of Systems (Focused)
+
+[Focus on systems relevant to consultation question]
+
+**[Relevant system]:** [Findings]  
+**[Additional relevant systems]:** [Findings]
+
+---
+
+## Physical Examination
+
+**Vital Signs:**
+- Temperature: _____ °F
+- Blood Pressure: _____/_____ mmHg
+- Heart Rate: _____ bpm
+- Respiratory Rate: _____ breaths/min
+- Oxygen Saturation: _____% on [O2 status]
+- Weight: _____ kg (if relevant)
+
+**General:**  
+[Overall appearance, distress level]
+
+**[Focused Examination Relevant to Consultation]:**
+
+**Example for Cardiology Consult:**
+- **Cardiovascular:**
+  - JVP: [cm H2O]
+  - PMI: [location]
+  - Heart sounds: [S1, S2, murmurs, gallops, rubs]
+  - Peripheral pulses: [quality]
+  - Edema: [location and severity]
+
+**Example for Pulmonary Consult:**
+- **Pulmonary:**
+  - Respiratory effort: [description]
+  - Auscultation: [breath sounds, wheezes, crackles]
+  - Percussion: [findings]
+
+[Include other relevant systems, may abbreviate or defer non-pertinent systems]
+
+---
+
+## Pertinent Laboratory and Imaging Data
+
+**Labs ([Date]):**
+
+[Include only labs relevant to consultation]
+
+| Test | Result | Reference Range | Trend |
+|------|--------|----------------|-------|
+| [Relevant lab] | [Value] | [Range] | [↑/↓/→] |
+
+**Imaging/Diagnostics:**
+
+**[Study] ([Date]):** [Relevant findings]
+
+**ECG ([Date]):** [Relevant findings]
+
+**Other Studies:** [Relevant results]
+
+---
+
+## Assessment
+
+**Consultant's Assessment of [Specific Problem]:**
+
+[Detailed assessment of the consultation question]
+
+**Differential Diagnosis:**
+1. [Most likely diagnosis] - [supporting evidence]
+2. [Alternative diagnosis] - [evidence for/against]
+3. [Additional considerations]
+
+**Severity/Acuity:** [Assessment of severity]
+
+**Contributing Factors:** [What is contributing to the problem]
+
+**Prognosis:** [Short-term and long-term outlook]
+
+---
+
+## Recommendations
+
+**[Problem Being Addressed]:**
+
+**Diagnostic Recommendations:**
+1. [Specific test] - [Rationale]
+2. [Additional studies] - [Why needed]
+
+**Therapeutic Recommendations:**
+1. **[Intervention/Medication]:**
+   - [Specific dose, route, frequency]
+   - [Duration]
+   - [Rationale]
+   - [Monitoring parameters]
+
+2. **[Additional treatments]**
+
+3. **[Procedures if recommended]:**
+   - [Procedure name]
+   - [Indication]
+   - [Timing]
+
+**Monitoring Recommendations:**
+- [What to monitor]
+- [How often]
+- [Target parameters]
+
+**Follow-up Recommendations:**
+- [ ] Will follow along as consultant during hospitalization
+- [ ] Recommend follow-up in [Specialty] clinic in [timeframe]
+- [ ] Recommend re-consultation if [specific circumstances]
+- [ ] No further consultation needed unless [conditions]
+
+**Additional Recommendations:**
+- [Lifestyle modifications]
+- [Patient education points]
+- [Precautions]
+
+**Recommendations Summary for Primary Team:**
+[Concise bulleted list of key recommendations that can be quickly reviewed]
+1. [Action item 1]
+2. [Action item 2]
+3. [Action item 3]
+
+---
+
+## Consultantdiscussion with Primary Team
+
+**Discussed with:** [Name, role]  
+**Date/Time:** [MM/DD/YYYY at HH:MM]  
+**Topics discussed:** [Key points discussed]  
+**Plan agreed upon:** [Agreement or modifications]
+
+---
+
+## Follow-up Plan
+
+**Consultant will:**
+- [ ] Round daily until [condition met or discharge]
+- [ ] Re-evaluate in [X] days
+- [ ] Available for questions or changes in clinical status
+- [ ] Recommend outpatient follow-up in [timeframe]
+
+**Primary team to:**
+- [ ] Implement above recommendations
+- [ ] Notify consultant if [specific circumstances]
+- [ ] Monitor [specific parameters]
+
+---
+
+## Signature
+
+**Consultant:** [Name, MD/DO, credentials]  
+**Service:** [Consulting service]  
+**Date/Time:** [MM/DD/YYYY at HH:MM]  
+**Pager/Contact:** [Number]  
+**Signature:** ____________________
+
+**Co-signature (if fellow or resident):**  
+**Attending:** [Name, credentials]  
+**Date/Time:** [MM/DD/YYYY at HH:MM]  
+**Signature:** ____________________
+
+---
+
+## Template Notes
+
+**Key Principles for Consultation Notes:**
+
+1. **Answer the question:** Directly address the specific consultation request
+2. **Be focused:** Include only information relevant to the consultation
+3. **Be specific:** Provide clear, actionable recommendations
+4. **Be concise:** Respect primary team's time
+5. **Be available:** Make follow-up plan clear
+
+**Common Consultation Types:**
+
+**Cardiology:**
+- Pre-operative risk assessment
+- Arrhythmia management
+- Heart failure management
+- Chest pain evaluation
+
+**Nephrology:**
+- Acute kidney injury
+- Chronic kidney disease management
+- Electrolyte abnormalities
+- Dialysis initiation/management
+
+**Infectious Disease:**
+- Antibiotic selection
+- Fever of unknown origin
+- Complex infections
+- HIV management
+
+**Endocrinology:**
+- Diabetes management
+- Thyroid disorders
+- Adrenal insufficiency
+- Calcium disorders
+
+**Psychiatry:**
+- Capacity assessment
+- Depression/anxiety management
+- Agitation management
+- Substance withdrawal
+
+**Pain Management:**
+- Chronic pain consultation
+- Post-operative pain control
+- Cancer pain management
+
+**Palliative Care:**
+- Goals of care discussion
+- Symptom management
+- End-of-life care planning
+
+**Tips for Effective Consultations:**
+
+- Call the referring provider before seeing patient to clarify question
+- Introduce yourself to patient and explain your role
+- Review chart thoroughly before examination
+- Be respectful of primary team's care
+- Make specific recommendations, not vague suggestions
+- Document same day as consultation
+- Communicate recommendations verbally when appropriate
+- Be available for questions
+- Follow up consistently if ongoing consultation
+
+