scientific-writer 2.3.1__py3-none-any.whl

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

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+# HIPAA Compliance Checklist for Clinical Reports
+
+## 18 HIPAA Identifiers - De-identification Checklist
+
+Verify that ALL of the following identifiers have been removed or altered:
+
+- [ ] **1. Names** - Patient name, family members, healthcare providers (unless necessary and consented)
+
+- [ ] **2. Geographic subdivisions smaller than state**
+  - No street addresses
+  - No cities (unless >20,000 population and part of ZIP can be kept if >20,000)
+  - No counties  
+  - First 3 digits of ZIP code acceptable only if geographic unit >20,000 people
+  - All other portions of ZIP codes removed
+
+- [ ] **3. Dates** (except year)
+  - No exact dates of birth (year only acceptable; year of birth for those >89 must be aggregated)
+  - No admission dates
+  - No discharge dates
+  - No dates of service
+  - No dates of death
+  - Use relative time periods (e.g., "3 months prior") or years only
+
+- [ ] **4. Telephone numbers**
+  - No phone numbers of any kind
+  - Including patient, family, provider contact numbers
+
+- [ ] **5. Fax numbers**
+  - No fax numbers
+
+- [ ] **6. Email addresses**
+  - No email addresses for patient or related individuals
+
+- [ ] **7. Social Security numbers**
+  - No SSN or partial SSN
+
+- [ ] **8. Medical record numbers**
+  - No MRN, hospital ID, or clinic numbers
+  - Use coded study ID or case number if needed
+
+- [ ] **9. Health plan beneficiary numbers**
+  - No insurance ID numbers
+  - No policy numbers
+
+- [ ] **10. Account numbers**
+  - No billing account numbers
+  - No financial account information
+
+- [ ] **11. Certificate/license numbers**
+  - No driver's license numbers
+  - No professional license numbers (unless for author credentials)
+
+- [ ] **12. Vehicle identifiers and serial numbers**
+  - No license plate numbers
+  - No VIN numbers
+
+- [ ] **13. Device identifiers and serial numbers**
+  - No pacemaker serial numbers
+  - No implant device serial numbers
+  - Generic device description acceptable (e.g., "implantable cardioverter-defibrillator")
+
+- [ ] **14. Web URLs**
+  - No personal websites
+  - No URLs identifying individuals
+
+- [ ] **15. IP addresses**
+  - No IP addresses
+
+- [ ] **16. Biometric identifiers**
+  - No fingerprints
+  - No voiceprints
+  - No retinal scans
+  - No other biometric data
+
+- [ ] **17. Full-face photographs and comparable images**
+  - No full-face photographs without consent
+  - Crop or blur faces if showing
+  - Remove identifying features (jewelry, tattoos, birthmarks if not clinically relevant)
+  - Black bars over eyes NOT sufficient
+  - Ensure no reflection or background identification
+
+- [ ] **18. Any other unique identifying characteristic or code**
+  - No unique characteristics that could identify individual
+  - No rare disease combinations that could identify
+  - Consider if combination of remaining data points could identify individual
+
+---
+
+## Additional De-identification Considerations
+
+### Ages and Dates
+
+- [ ] Patients aged ≤89: Exact age or age range acceptable
+- [ ] Patients aged >89: Must be aggregated to "90 or older" or ">89 years"
+- [ ] Dates: Use only years OR use relative time periods
+  - Example: "3 months prior to presentation" instead of "on January 15, 2023"
+  - Example: "admitted in 2023" instead of "admitted on March 10, 2023"
+
+### Geographic Information
+
+- [ ] State or country is acceptable
+- [ ] Removed specific cities (unless population >20,000 and no other identifying information)
+- [ ] Removed hospital/clinic names
+- [ ] Use general descriptors: "a community hospital in the Midwest" or "a tertiary care center"
+
+### Rare Conditions and Combinations
+
+- [ ] Consider if very rare disease alone could identify patient
+- [ ] Consider if combination of:
+  - Age + diagnosis + geographic area + timeframe could identify patient
+- [ ] May need to be vague about certain unique details
+- [ ] Balance between providing clinical information and protecting privacy
+
+### Images and Figures
+
+- [ ] All patient identifiers removed from image headers/metadata
+- [ ] DICOM data stripped
+- [ ] Dates removed from images
+- [ ] Medical record numbers removed
+- [ ] Faces cropped, blurred, or obscured
+- [ ] Identifying marks removed or obscured:
+  - Tattoos
+  - Jewelry
+  - Birthmarks or unique scars (if not clinically relevant)
+- [ ] Scale bars and annotations do not contain identifying information
+- [ ] Background environment de-identified (room numbers, nameplates, etc.)
+
+### Voice and Video
+
+- [ ] No audio recordings with patient voice (unless consent obtained)
+- [ ] No video showing identifiable features (unless consent obtained)
+- [ ] If video necessary, face must be obscured
+
+---
+
+## Informed Consent Checklist (for Case Reports/Publications)
+
+### Consent Requirements
+
+- [ ] Informed consent obtained BEFORE publication submission
+- [ ] Consent obtained from patient directly (if capable)
+- [ ] If patient deceased or incapacitated, consent from legal representative or next of kin
+- [ ] For pediatric cases, parental/guardian consent obtained
+
+### Consent Form Elements
+
+The informed consent form must include:
+
+- [ ] Purpose of publication (education, medical knowledge)
+- [ ] What will be published (case details, images, outcomes)
+- [ ] Journal or publication venue (if known)
+- [ ] Open access vs. subscription (public availability)
+- [ ] De-identification efforts explained
+- [ ] Potential for re-identification acknowledged
+- [ ] No effect on clinical care
+- [ ] Right to withdraw consent (timing limitations)
+- [ ] Contact information for questions
+- [ ] Patient signature and date
+- [ ] Witness signature (if required)
+
+### Consent Documentation
+
+- [ ] Signed consent form on file
+- [ ] Copy provided to patient
+- [ ] Consent available for editor review
+- [ ] Statement in manuscript confirming consent obtained
+
+**Example statement for manuscript:**
+"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."
+
+---
+
+## Safe Harbor vs. Expert Determination
+
+### Safe Harbor Method
+
+- [ ] All 18 identifiers removed
+- [ ] No actual knowledge that remaining information could identify individual
+- [ ] Most straightforward method
+- [ ] Recommended for most clinical reports
+
+### Expert Determination Method
+
+- [ ] Qualified statistician/expert determined very small re-identification risk
+- [ ] Methodology documented
+- [ ] Analysis methods specified
+- [ ] Conclusion documented
+- [ ] May allow retention of some data elements
+- [ ] Requires statistical expertise
+
+**Method used:** [ ] Safe Harbor  [ ] Expert Determination
+
+---
+
+## Minimum Necessary Standard
+
+### Use and Disclosure
+
+- [ ] Only minimum PHI necessary for purpose is used
+- [ ] Purpose of disclosure clearly defined
+- [ ] Limited to relevant information only
+- [ ] Consider de-identified data or limited data set as alternatives
+
+### Exceptions to Minimum Necessary
+
+Minimum necessary does NOT apply to:
+- Treatment purposes (providers may need full information)
+- Patient-authorized disclosures
+- Disclosures required by law
+- Disclosures to HHS for compliance investigation
+
+---
+
+## Authorization for Use/Disclosure of PHI
+
+### When Authorization Required
+
+Authorization needed for:
+- [ ] Research (unless IRB waiver granted)
+- [ ] Marketing purposes
+- [ ] Sale of PHI
+- [ ] Psychotherapy notes
+- [ ] Uses beyond treatment, payment, operations (TPO)
+
+### Authorization Elements
+
+If authorization required, it must include:
+
+- [ ] Specific description of PHI to be used/disclosed
+- [ ] Person(s) authorized to make disclosure
+- [ ] Person(s) to receive information
+- [ ] Purpose of disclosure
+- [ ] Expiration date or event
+- [ ] Right to revoke and how
+- [ ] Right to refuse to sign
+- [ ] Potential for re-disclosure by recipient
+- [ ] Patient signature and date
+
+---
+
+## Limited Data Set
+
+### Limited Data Set Option
+
+A limited data set removes 16 of 18 identifiers but may retain:
+- [ ] Dates (admission, discharge, service, birth, death)
+- [ ] Geographic information (city, state, ZIP code)
+
+### Requirements for Limited Data Set
+
+- [ ] Data Use Agreement (DUA) required
+- [ ] DUA specifies permitted uses
+- [ ] Only for research, public health, or healthcare operations
+- [ ] Recipient agrees not to re-identify
+- [ ] Recipient agrees to safeguard data
+
+---
+
+## Security Safeguards Checklist
+
+### Administrative Safeguards
+
+- [ ] Security management process in place
+- [ ] Workforce security measures
+- [ ] Access management (role-based)
+- [ ] Security training for workforce
+- [ ] Incident response procedures
+
+### Physical Safeguards
+
+- [ ] Facility access controls
+- [ ] Workstation use policies
+- [ ] Workstation security measures
+- [ ] Device and media controls
+- [ ] Secure disposal procedures
+
+### Technical Safeguards
+
+- [ ] Access controls (unique user IDs, passwords)
+- [ ] Audit controls and logging
+- [ ] Integrity controls
+- [ ] Transmission security (encryption)
+- [ ] Automatic logoff after inactivity
+
+---
+
+## Breach Notification Checklist
+
+### If Unauthorized Disclosure Occurs
+
+- [ ] Determine if breach occurred (unauthorized access/use/disclosure)
+- [ ] Assess risk of harm to individual
+- [ ] If breach affects <500 individuals:
+  - Notify individual within 60 days
+  - Report to HHS annually
+- [ ] If breach affects ≥500 individuals:
+  - Notify individuals within 60 days
+  - Notify HHS within 60 days
+  - Notify media if affects ≥500 in a state/jurisdiction
+- [ ] Document breach and response
+- [ ] Implement corrective action
+
+### Breach Notification Content
+
+Notification must include:
+- [ ] Description of breach
+- [ ] Types of information involved
+- [ ] Steps individuals should take
+- [ ] What organization is doing
+- [ ] Contact for questions
+
+---
+
+## Research-Specific Compliance
+
+### IRB/Privacy Board Considerations
+
+- [ ] IRB approval obtained (if research)
+- [ ] HIPAA authorization obtained OR waiver granted
+- [ ] Waiver justification documented:
+  - Minimal risk to privacy
+  - Research cannot practically be conducted without waiver
+  - Research cannot practically be conducted without PHI
+  - Plan to protect identifiers
+  - Plan to destroy identifiers when appropriate
+
+### Clinical Trial Reporting
+
+- [ ] Subject identified by ID number only
+- [ ] No names in regulatory submissions
+- [ ] Initials only if required by regulatory authority
+- [ ] Dates limited to year or relative time
+- [ ] Protocol includes privacy protections
+
+---
+
+## Special Populations
+
+### Pediatric Cases
+
+- [ ] Parent/guardian consent obtained
+- [ ] Child assent obtained (if age-appropriate)
+- [ ] Extra care with identifiable photos
+- [ ] School information removed
+
+### Deceased Patients
+
+- [ ] HIPAA protections apply for 50 years post-death
+- [ ] Next of kin consent for publication
+- [ ] Autopsy information de-identified
+
+### Mental Health and Substance Abuse
+
+- [ ] Extra protections under 42 CFR Part 2
+- [ ] Explicit consent for disclosure
+- [ ] Cannot re-disclose without consent
+
+---
+
+## Final Compliance Verification
+
+**Reviewed by:** ____________________  
+**Date:** ____________________  
+**Signature:** ____________________
+
+**Compliance Status:** [ ] Compliant  [ ] Needs revision  [ ] Not compliant
+
+**Issues identified:**
+1. [Issue]
+2. [Issue]
+
+**Corrective actions:**
+1. [Action]
+2. [Action]
+
+**Re-review required:** [ ] Yes  [ ] No  
+**Re-review date:** ____________________
+
+---
+
+## Documentation to Maintain
+
+Keep on file:
+- [ ] Signed patient consent (if applicable)
+- [ ] IRB approval (if research)
+- [ ] HIPAA waiver (if applicable)
+- [ ] De-identification verification
+- [ ] Data use agreement (if limited data set)
+- [ ] Authorization forms (if applicable)
+- [ ] Training records for personnel handling PHI
+- [ ] Audit logs
+
+**Retention period:** Minimum 6 years per HIPAA requirement
+
+

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

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+# History and Physical Examination (H&P) Template
+
+**Patient Name:** [Last, First]  
+**Medical Record Number:** [MRN]  
+**Date of Birth:** [MM/DD/YYYY]  
+**Age:** [years]  
+**Sex:** [M/F]
+
+**Date of Admission/Encounter:** [MM/DD/YYYY]  
+**Time:** [HH:MM]  
+**Location:** [Hospital floor, Clinic, ED]  
+**Admitting Service:** [Medicine, Surgery, etc.]  
+**Attending Physician:** [Name]
+
+---
+
+## Chief Complaint (CC)
+
+"[Patient's stated reason for seeking care, in quotes]"
+
+---
+
+## History of Present Illness (HPI)
+
+[Patient Name] is a [age]-year-old [sex] with a history of [relevant PMHx] who presents with [chief complaint].
+
+[Use OPQRST format for symptoms, provide chronological narrative]
+
+**Onset:** [When did symptoms start? Sudden vs gradual onset?]  
+**Location:** [Where? Does it radiate?]  
+**Duration:** [How long?]  
+**Character:** [Quality - sharp, dull, pressure, etc.]  
+**Aggravating factors:** [What makes it worse?]  
+**Relieving factors:** [What makes it better?]  
+**Timing:** [Constant or intermittent? Pattern?]  
+**Severity:** [0-10 scale for pain, functional impact]  
+**Associated symptoms:** [Other symptoms?]
+
+**Prior evaluations and treatments:**  
+**Why presenting now:**
+
+---
+
+## Past Medical History (PMH)
+
+1. [Condition] - diagnosed [year], [current status]
+2. [Condition] - diagnosed [year], [treatment]
+3. [Additional conditions]
+
+[ ] No known medical problems
+
+---
+
+## Past Surgical History (PSH)
+
+1. [Procedure] ([year]) - [indication, complications if any]
+2. [Procedure] ([year])
+
+[ ] No prior surgeries
+
+---
+
+## Medications
+
+| Medication | Dose | Route | Frequency | Indication |
+|------------|------|-------|-----------|------------|
+| [Drug name] | [mg] | [PO/IV/etc] | [BID/etc] | [Why prescribed] |
+
+[ ] No current medications
+
+---
+
+## Allergies
+
+| Allergen | Reaction |
+|----------|----------|
+| [Drug/Food/Environmental] | [Type of reaction] |
+
+[ ] No known drug allergies (NKDA)
+
+---
+
+## Family History (FH)
+
+- **Father:** [Age/deceased at age X], [medical conditions]
+- **Mother:** [Age/deceased at age X], [medical conditions]
+- **Siblings:** [Number], [relevant conditions]
+- **Children:** [Number], [relevant conditions]
+
+[Note hereditary conditions relevant to patient's presentation]
+
+[ ] Non-contributory
+
+---
+
+## Social History (SH)
+
+**Tobacco:** [Current/former/never], [pack-years if applicable]  
+**Alcohol:** [Frequency and amount, CAGE questions if indicated]  
+**Illicit drugs:** [Current/former/never, type, route]  
+**Occupation:** [Current or former occupation]  
+**Living situation:** [Lives alone/with family, housing type]  
+**Marital status:** [Single/married/divorced/widowed]  
+**Sexual history:** [If relevant]  
+**Exercise:** [Type and frequency]  
+**Diet:** [General diet description]  
+**Functional status:** [ADL independence, baseline activity level]
+
+---
+
+## Review of Systems (ROS)
+
+[Systematic review - check relevant systems]
+
+**Constitutional:** [ ] Fever [ ] Chills [ ] Night sweats [ ] Weight loss [ ] Weight gain [ ] Fatigue  
+**Eyes:** [ ] Vision changes [ ] Eye pain [ ] Discharge  
+**ENT:** [ ] Hearing loss [ ] Tinnitus [ ] Sinus problems [ ] Sore throat  
+**Cardiovascular:** [ ] Chest pain [ ] Palpitations [ ] Edema [ ] Orthopnea [ ] PND [ ] Claudication  
+**Respiratory:** [ ] Dyspnea [ ] Cough [ ] Wheezing [ ] Hemoptysis  
+**Gastrointestinal:** [ ] Nausea [ ] Vomiting [ ] Diarrhea [ ] Constipation [ ] Abdominal pain [ ] Melena [ ] Hematochezia  
+**Genitourinary:** [ ] Dysuria [ ] Frequency [ ] Urgency [ ] Hematuria [ ] Incontinence  
+**Musculoskeletal:** [ ] Joint pain [ ] Swelling [ ] Stiffness [ ] Back pain [ ] Weakness  
+**Skin:** [ ] Rash [ ] Lesions [ ] Itching [ ] Changes in moles  
+**Neurological:** [ ] Headache [ ] Dizziness [ ] Syncope [ ] Seizures [ ] Weakness [ ] Numbness [ ] Tingling  
+**Psychiatric:** [ ] Depression [ ] Anxiety [ ] Sleep disturbance  
+**Endocrine:** [ ] Heat/cold intolerance [ ] Polyuria [ ] Polydipsia [ ] Polyphagia  
+**Hematologic/Lymphatic:** [ ] Easy bruising [ ] Bleeding [ ] Lymph node swelling  
+**Allergic/Immunologic:** [ ] Seasonal allergies [ ] Frequent infections
+
+**All other systems reviewed and negative** [ ]
+
+---
+
+## Physical Examination
+
+**Vital Signs:**
+- Temperature: _____ °F (oral/axillary/tympanic)
+- Blood Pressure: _____/_____ mmHg ([right arm, sitting])
+- Heart Rate: _____ bpm (regular/irregular)
+- Respiratory Rate: _____ breaths/min
+- Oxygen Saturation: _____% on [room air / O2 at ___ L/min]
+- Height: _____ cm / inches
+- Weight: _____ kg / lbs
+- BMI: _____ kg/m²
+- Pain Score: ___/10
+
+**General:**  
+[Overall appearance, apparent vs stated age, nutritional status, distress level]
+
+**HEENT:**
+- Head: [Normocephalic, atraumatic, scalp lesions]
+- Eyes: [PERRLA, EOMI, conjunctiva, sclera, fundoscopy if done]
+- Ears: [TMs, canals, hearing]
+- Nose: [Nares, septum, discharge, sinus tenderness]
+- Throat: [Oropharynx, tonsils, dentition, mucosa]
+
+**Neck:**  
+[Supple/stiff, lymphadenopathy, thyroid, JVP, carotid bruits]
+
+**Cardiovascular:**
+- Inspection: [PMI, precordial movement]
+- Palpation: [PMI location, thrills, lifts]
+- Auscultation: [Rate, rhythm, S1/S2, murmurs/rubs/gallops, location and radiation]
+- Peripheral pulses: [Radial, femoral, DP, PT - rate quality bilaterally]
+- Extremities: [Edema, cyanosis, clubbing]
+
+**Pulmonary:**
+- Inspection: [Respiratory effort, use of accessory muscles, chest wall deformities]
+- Palpation: [Tactile fremitus, chest expansion]
+- Percussion: [Resonance, dullness]
+- Auscultation: [Breath sounds, adventitious sounds - location and quality]
+
+**Abdomen:**
+- Inspection: [Contour, scars, distention, visible peristalsis]
+- Auscultation: [Bowel sounds - present, hyperactive, hypoactive, absent]
+- Percussion: [Tympany, dullness, liver span, spleen]
+- Palpation: [Soft/firm, tenderness, masses, organomegaly, rebound, guarding, Murphy's sign]
+
+**Musculoskeletal:**
+- Inspection: [Deformities, swelling, erythema]
+- Palpation: [Tenderness, warmth]
+- Range of motion: [Active and passive, limitations]
+- Strength: [5-point scale by major muscle groups]
+- Gait: [Normal, antalgic, ataxic, spastic]
+
+**Skin:**  
+[Color, temperature, moisture, turgor, lesions, rashes, wounds]
+
+**Neurological:**
+- Mental Status: [Alert, oriented x3 (person, place, time), speech, memory]
+- Cranial Nerves: [II-XII - document abnormalities]
+- Motor: [Strength 5-point scale, tone, bulk, fasciculations]
+- Sensory: [Light touch, pinprick, proprioception, vibration]
+- Reflexes: [Deep tendon reflexes 0-4+ scale, Babinski]
+- Coordination: [Finger-to-nose, heel-to-shin, rapid alternating movements]
+- Gait: [Already documented above or describe here]
+
+**Psychiatric:**  
+[Mood, affect, thought process, thought content, judgment, insight]
+
+**Genitourinary:** (if applicable)  
+[Defer/document findings if examined]
+
+**Rectal:** (if applicable)  
+[Defer/document findings if examined]
+
+---
+
+## Laboratory and Imaging Results
+
+[Include relevant results available at time of H&P]
+
+**Labs ([Date]):**
+
+| Test | Result | Reference Range | Flag |
+|------|--------|----------------|------|
+| WBC | [Value] | [Range] | [H/L/-] |
+| Hemoglobin | [Value] | [Range] | [H/L/-] |
+| [Additional labs] | | | |
+
+**Imaging ([Study], [Date]):**  
+[Key findings]
+
+**ECG ([Date]):**  
+[Rate, rhythm, intervals, axis, ST-T changes, other findings]
+
+**Other Studies:**
+
+---
+
+## Assessment and Plan
+
+**Assessment:**
+
+[Patient summary statement in one sentence]
+
+**Problem List:**
+
+**1. [Primary Problem/Diagnosis] ([ICD-10 code])**
+
+**Assessment:** [Brief description of problem, severity, stability]
+
+**Plan:**
+- **Diagnostics:** [Labs, imaging, consultations needed]
+- **Therapeutics:** [Medications, procedures, interventions]
+  - [Medication]: [dose, route, frequency] for [indication]
+- **Monitoring:** [What to monitor, how often]
+- **Follow-up:** [When and with whom]
+- **Disposition:** [Admit to floor/ICU, discharge, observation]
+
+**2. [Secondary Problem] ([ICD-10 code])**
+
+**Assessment:** [Description]
+
+**Plan:**
+- [Diagnostics]
+- [Therapeutics]
+- [Monitoring]
+
+**3. [Additional Problems]**
+[Continue for all active problems]
+
+**Code Status:** [Full code / DNR / DNI / Other]
+
+**Prophylaxis:**
+- DVT prophylaxis: [Pharmacologic and/or mechanical]
+- GI prophylaxis: [If indicated]
+- Aspiration precautions: [If indicated]
+
+**Disposition:** [Admit to service, location (floor/ICU), level of care]
+
+---
+
+## Signature
+
+**Physician:** [Name, credentials]  
+**Level:** [Intern, Resident, Attending]  
+**Date/Time:** [MM/DD/YYYY at HH:MM]  
+**Signature:** ____________________
+
+**Co-signature (if applicable):**  
+**Attending:** [Name, credentials]  
+**Date/Time:** [MM/DD/YYYY at HH:MM]  
+**Signature:** ____________________
+
+---
+
+## Template Completion Checklist
+
+- [ ] Chief complaint documented
+- [ ] HPI comprehensive (≥4 HPI elements for billing)
+- [ ] PMH reviewed
+- [ ] Medications reconciled
+- [ ] Allergies documented
+- [ ] ROS performed (≥10 systems for comprehensive)
+- [ ] Complete physical exam documented (≥8 systems for comprehensive)
+- [ ] Labs/imaging reviewed
+- [ ] Assessment and plan for each problem
+- [ ] Code status documented
+- [ ] Prophylaxis addressed
+- [ ] Disposition clear
+- [ ] Completed within 24 hours of admission (TJC requirement)
+- [ ] Signed and dated
+
+