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

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

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+# Laboratory Report Template
+
+## Patient Information
+
+**Patient Name:** [Last, First]  
+**Medical Record Number:** [MRN]  
+**Date of Birth:** [MM/DD/YYYY]  
+**Age/Sex:** [Age years, M/F]
+
+**Ordering Physician:** [Name]  
+**Location:** [Inpatient unit / Outpatient clinic]
+
+---
+
+## Specimen Information
+
+**Specimen Type:** [Blood / Serum / Plasma / Urine / CSF / Other]  
+**Collection Date/Time:** [MM/DD/YYYY at HH:MM]  
+**Received Date/Time:** [MM/DD/YYYY at HH:MM]  
+**Reported Date/Time:** [MM/DD/YYYY at HH:MM]
+
+**Accession Number:** [Lab accession number]  
+**Specimen Condition:** [Acceptable / See comments]  
+**Fasting Status:** [Fasting / Non-fasting / Unknown] (if relevant)
+
+---
+
+## Laboratory Results
+
+| Test Name | Result | Units | Reference Range | Flag |
+|-----------|--------|-------|----------------|------|
+| [Test] | [Value] | [Unit] | [Normal range] | [L/H/Critical] |
+
+### Example: Complete Blood Count (CBC)
+
+| Test | Result | Units | Reference Range | Flag |
+|------|--------|-------|----------------|------|
+| White Blood Cell Count | 12.5 | × 10³/μL | 4.5-11.0 | H |
+| Hemoglobin | 10.2 | g/dL | 12.0-16.0 (F), 14.0-18.0 (M) | L |
+| Hematocrit | 31.5 | % | 36.0-48.0 (F), 42.0-52.0 (M) | L |
+| Platelet Count | 245 | × 10³/μL | 150-400 | - |
+| MCV | 88.5 | fL | 80.0-100.0 | - |
+| MCH | 29.5 | pg | 27.0-33.0 | - |
+| MCHC | 33.2 | g/dL | 32.0-36.0 | - |
+| RDW | 14.5 | % | 11.5-14.5 | - |
+
+**Differential:**
+| Cell Type | Result | Units | Reference Range | Flag |
+|-----------|--------|-------|----------------|------|
+| Neutrophils | 75 | % | 40-70 | H |
+| Lymphocytes | 15 | % | 20-40 | L |
+| Monocytes | 7 | % | 2-10 | - |
+| Eosinophils | 2 | % | 1-4 | - |
+| Basophils | 1 | % | 0-2 | - |
+
+### Example: Basic Metabolic Panel (BMP)
+
+| Test | Result | Units | Reference Range | Flag |
+|------|--------|-------|----------------|------|
+| Sodium | 138 | mEq/L | 136-145 | - |
+| Potassium | 3.2 | mEq/L | 3.5-5.0 | L |
+| Chloride | 102 | mEq/L | 98-107 | - |
+| CO2 | 24 | mEq/L | 22-30 | - |
+| Blood Urea Nitrogen | 28 | mg/dL | 7-20 | H |
+| Creatinine | 1.8 | mg/dL | 0.6-1.2 (F), 0.7-1.3 (M) | H |
+| Glucose | 145 | mg/dL | 70-100 (fasting) | H |
+| eGFR | 42 | mL/min/1.73m² | >60 | L |
+
+---
+
+## Interpretation / Comments
+
+[Clinical interpretation when applicable]
+
+**Example for Anemia:**
+```
+Normocytic anemia with elevated WBC. Differential diagnosis includes anemia of chronic 
+disease, recent blood loss, or hemolysis. Consider reticulocyte count, iron studies, 
+and peripheral smear for further evaluation. Clinical correlation recommended.
+```
+
+**Example for Electrolyte Abnormality:**
+```
+Hypokalemia detected (K+ 3.2 mEq/L). Common causes include diuretic use, GI losses, or 
+inadequate intake. Recommend potassium repletion and follow-up testing. Moderate 
+azotemia present, consistent with acute kidney injury or chronic kidney disease. 
+Clinical correlation with patient history and prior results recommended.
+```
+
+---
+
+## Critical Values
+
+[If any results meet criteria for critical values]
+
+**Critical Result:** [Test name] = [Value] [Units]  
+**Reference Range:** [Normal range]  
+**Significance:** [Life-threatening, requires immediate action]
+
+**Notification:**
+- **Called to:** [Name and title of person notified]
+- **Date/Time:** [MM/DD/YYYY at HH:MM]
+- **Read-back verified:** [Yes]
+- **Notified by:** [Lab personnel name]
+
+**Example Critical Values:**
+- Glucose <40 mg/dL or >500 mg/dL
+- Potassium <2.5 mEq/L or >6.5 mEq/L
+- Sodium <120 mEq/L or >160 mEq/L
+- Hemoglobin <5.0 g/dL
+- Platelets <20 × 10³/μL
+- WBC <1.0 × 10³/μL or >50 × 10³/μL
+- INR >5.0 (on warfarin)
+- Positive blood culture
+- Positive CSF Gram stain
+
+---
+
+## Quality Control
+
+**Specimen Quality:** [Acceptable / See note]
+
+**QC Notes:**
+- [X] Specimen collected in appropriate tube
+- [X] Specimen adequately labeled
+- [X] Specimen volume sufficient
+- [X] No hemolysis, lipemia, or icterus
+- [X] Specimen processed within acceptable time
+
+**Issues (if any):**
+- [ ] Hemolyzed - may affect [specific tests]
+- [ ] Clotted - unable to perform coagulation studies
+- [ ] Insufficient volume - limited testing performed
+- [ ] Delayed processing - stability concerns for [specific analytes]
+
+---
+
+## Methodology
+
+**Test Method:** [Instrumentation and methodology]
+
+Examples:
+- **CBC:** Automated cell counter (Sysmex XN-1000)
+- **Chemistry:** Spectrophotometry (Beckman AU5800)
+- **Glucose:** Enzymatic assay, hexokinase method
+- **HbA1c:** HPLC (high-performance liquid chromatography)
+- **Troponin:** High-sensitivity immunoassay
+- **Drug levels:** Liquid chromatography-mass spectrometry (LC-MS/MS)
+
+---
+
+## Special Tests Examples
+
+### Hemoglobin A1c
+
+| Test | Result | Units | Interpretation |
+|------|--------|-------|----------------|
+| HbA1c | 8.5 | % | Consistent with poorly controlled diabetes |
+| HbA1c | 8.5 | % (69 mmol/mol) | Target <7% for most patients |
+
+**Reference Ranges:**
+- Non-diabetic: 4.0-5.6%
+- Prediabetes: 5.7-6.4%
+- Diabetes diagnosis: ≥6.5%
+- Treatment target: <7% (individualized)
+
+### Lipid Panel
+
+| Test | Result | Units | Reference Range | Desirable |
+|------|--------|-------|----------------|-----------|
+| Total Cholesterol | 245 | mg/dL | - | <200 |
+| LDL Cholesterol | 160 | mg/dL | - | <100 |
+| HDL Cholesterol | 38 | mg/dL | - | >40 (M), >50 (F) |
+| Triglycerides | 235 | mg/dL | - | <150 |
+| VLDL Cholesterol (calc) | 47 | mg/dL | - | <30 |
+
+### Coagulation Studies
+
+| Test | Result | Units | Reference Range | Flag |
+|------|--------|-------|----------------|------|
+| PT | 18.5 | seconds | 11.0-13.5 | H |
+| INR | 2.8 | ratio | 0.8-1.2 | H |
+| PTT | 42 | seconds | 25-35 | H |
+
+**Therapeutic Ranges (INR):**
+- Atrial fibrillation: 2.0-3.0
+- Mechanical heart valve: 2.5-3.5
+- DVT/PE treatment: 2.0-3.0
+
+### Thyroid Function Tests
+
+| Test | Result | Units | Reference Range | Flag |
+|------|--------|-------|----------------|------|
+| TSH | 8.5 | μIU/mL | 0.4-4.0 | H |
+| Free T4 | 0.7 | ng/dL | 0.8-1.8 | L |
+| Free T3 | 2.1 | pg/mL | 2.3-4.2 | L |
+
+**Interpretation:** Findings consistent with primary hypothyroidism
+
+### Urinalysis
+
+**Physical Examination:**
+- Color: [Yellow / Amber / Other]
+- Clarity: [Clear / Cloudy / Turbid]
+- Specific Gravity: [1.005-1.030]
+
+**Chemical Examination:**
+| Test | Result | Reference |
+|------|--------|-----------|
+| pH | 6.0 | 5.0-8.0 |
+| Protein | Trace | Negative |
+| Glucose | Negative | Negative |
+| Ketones | Negative | Negative |
+| Blood | 2+ | Negative |
+| Bilirubin | Negative | Negative |
+| Urobilinogen | Normal | Normal |
+| Nitrite | Negative | Negative |
+| Leukocyte Esterase | Positive | Negative |
+
+**Microscopic Examination (if indicated):**
+- WBCs: [number] /hpf (normal <5)
+- RBCs: [number] /hpf (normal <3)
+- Epithelial cells: [Few/Moderate/Many]
+- Bacteria: [None/Few/Moderate/Many]
+- Casts: [Type and number]
+- Crystals: [Type if present]
+
+---
+
+## Microbiology Report Format
+
+### Culture Results
+
+**Specimen Source:** [Blood / Urine / Sputum / Wound / Other]  
+**Collection:** [Date and time]
+
+**Gram Stain:**
+[Results of Gram stain if performed]
+Example: "Many Gram-positive cocci in clusters, many WBCs"
+
+**Culture Results:**
+
+**Organism:** [Identified organism]  
+**Quantity:** [Light / Moderate / Heavy growth] or [CFU count]
+
+**Antimicrobial Susceptibility Testing:**
+
+| Antibiotic | Result | MIC (μg/mL) |
+|------------|--------|-------------|
+| [Drug name] | S/I/R | [Value] |
+
+Example:
+| Antibiotic | Result | MIC |
+|------------|--------|-----|
+| Ampicillin | R | >16 |
+| Ceftriaxone | S | ≤1 |
+| Levofloxacin | S | 0.5 |
+| Vancomycin | S | 1 |
+
+**Interpretation:** S = Susceptible, I = Intermediate, R = Resistant
+
+---
+
+## Molecular/Genetic Testing
+
+**Test:** [Specific test name]  
+**Method:** [PCR / Sequencing / Array / Other]  
+**Result:** [Detected / Not detected / Variant identified]
+
+**Interpretation:**
+[Clinical significance of result]
+
+---
+
+## Reference Laboratory Results
+
+[For send-out tests]
+
+**Test:** [Name]  
+**Performed by:** [Reference lab name and location]  
+**Result:** [Value]  
+**Reference Range:** [Range]  
+**Method:** [Methodology]  
+**Reported:** [Date]
+
+---
+
+## Laboratory Director Signature
+
+**Medical Director:**  
+[Name, MD]  
+[Board Certifications]  
+[CLIA License Number]
+
+**Electronically signed:** [Date]
+
+---
+
+## LOINC Codes (for interoperability)
+
+[LOINC codes for each test when applicable for electronic reporting]
+
+Example:
+- Hemoglobin: 718-7
+- Glucose: 2345-7
+- Creatinine: 2160-0
+- TSH: 3016-3
+
+

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

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+# Surgical Pathology Report Template
+
+## Patient and Specimen Information
+
+**Patient Name:** [Last, First]  
+**Medical Record Number:** [MRN]  
+**Date of Birth:** [MM/DD/YYYY]  
+**Age:** [years]  
+**Sex:** [M/F]
+
+**Accession Number:** [PathologyAccessionNumber]  
+**Specimen Received:** [Date and time]  
+**Report Date:** [Date]
+
+**Ordering Physician:** [Name]  
+**Clinical Service:** [Department]
+
+---
+
+## Specimen(s) Submitted
+
+**Specimen A:** [Description of specimen]  
+Example: "Skin, left forearm, excisional biopsy"
+
+**Specimen B:** [If multiple specimens]
+
+---
+
+## Clinical History / Indication
+
+[Relevant clinical information provided by clinician]
+
+Example: "72-year-old woman with enlarging pigmented lesion on left forearm. Clinical concern for melanoma. Previous biopsy showed atypical melanocytic proliferation."
+
+---
+
+## Gross Description
+
+**Specimen A labeled "[Specimen label]":**
+
+**Description:**
+- Received [fresh/in formalin]
+- Consists of [specimen type] measuring [dimensions in cm]
+- [External surface description]
+- [Cut surface/sectioning description]
+- [Lesion description if applicable]
+- [Orientation markers if present]
+- [Inking for margins]
+
+**Sampling:**
+- [How specimen was sectioned]
+- [Cassette labeling]
+- [Percent of tissue submitted]
+
+**Example:**
+```
+Specimen A labeled "Skin, left forearm, excisional biopsy":
+Received fresh is an oriented ellipse of skin measuring 3.5 x 1.2 x 0.8 cm with a 
+suture indicating superior. The epidermis contains a 1.1 cm diameter irregularly 
+pigmented lesion located 1.5 cm from superior, 1.2 cm from inferior, 0.8 cm from  
+medial, and 1.2 cm from lateral margins. Inking: superior blue, inferior black, 
+medial green, lateral red, deep yellow. Serially sectioned perpendicular to long 
+axis into 10 slices. Entirely submitted in cassettes A1-A4.
+```
+
+---
+
+## Microscopic Description
+
+[Detailed histological findings]
+
+**Architecture:**
+[Structural patterns observed]
+
+**Cytology:**
+[Cell type, nuclear features, cytoplasm, pleomorphism]
+
+**Special Features:**
+[Necrosis, mitoses, invasion, margins]
+
+**Stains/Immunohistochemistry Results:**
+[Results of special stains or immunostains]
+
+**Example:**
+```
+Sections show skin with an asymmetric melanocytic proliferation composed of 
+epithelioid and spindled melanocytes arranged in irregular nests at the 
+dermoepidermal junction with extension into the papillary and reticular dermis.
+Melanocytes show marked cytologic atypia with nuclear enlargement, hyperchromasia,
+and prominent nucleoli. Mitotic activity is present with 4 mitoses per mm². 
+No ulceration identified. The lesion extends to a Breslow depth of 1.8 mm 
+(Clark level IV). Margins are free of tumor (closest margin: deep, 0.3 cm).
+```
+
+---
+
+## Diagnosis
+
+**Specimen A, Skin, left forearm, excisional biopsy:**
+
+**[DIAGNOSIS IN CAPITAL LETTERS]**
+
+**Example Format:**
+```
+MALIGNANT MELANOMA, SUPERFICIAL SPREADING TYPE
+
+Pathologic features:
+- Breslow thickness: 1.8 mm
+- Clark level: IV
+- Mitotic rate: 4/mm²
+- Ulceration: Absent
+- Margins: Negative for melanoma (closest margin deep, 0.3 cm)
+- Lymphovascular invasion: Not identified
+- Perineural invasion: Not identified
+- Regression: Absent
+- Tumor-infiltrating lymphocytes: Present, non-brisk
+- Microsatellites: Absent
+```
+
+**For Cancer Specimens - Synoptic Format (CAP Protocol):**
+
+```
+SYNOPTIC REPORT FOR [CANCER TYPE]
+
+Procedure: [Type of resection]
+Tumor Site: [Specific location]
+Tumor Size: [Greatest dimension in cm]
+Histologic Type: [WHO classification]
+Histologic Grade: [Grading system and result]
+Depth of Invasion: [Measured in mm if applicable]
+Lymphovascular Invasion: [Present / Not identified]
+Perineural Invasion: [Present / Not identified]
+Margins:
+  - [Margin name]: [Negative/Positive, distance if negative]
+  - [All margins listed]
+Regional Lymph Nodes:
+  - Number examined: [X]
+  - Number with metastasis: [Y]
+  - Extranodal extension: [Present/Absent]
+Pathologic Stage (AJCC 8th edition): [pTNM]
+Additional Findings: [Other relevant findings]
+```
+
+---
+
+## Ancillary Studies
+
+**Immunohistochemistry:**
+
+| Antibody | Result | Interpretation |
+|----------|--------|----------------|
+| [Marker name] | [Positive/Negative, pattern] | [Clinical significance] |
+
+**Example:**
+| Antibody | Result | Interpretation |
+|----------|--------|----------------|
+| S100 | Positive, diffuse | Supports melanocytic lineage |
+| Melan-A | Positive, diffuse | Supports melanocytic lineage |
+| HMB-45 | Positive, patchy | Supports melanoma |
+| Ki-67 | 30% | High proliferative index |
+
+**Molecular/Genetic Testing:**
+[Results of molecular tests if performed]
+- BRAF mutation: [Detected/Not detected]
+- [Other relevant tests]
+
+---
+
+## Comment
+
+[Additional interpretive information, differential diagnosis, recommendations]
+
+**Example:**
+```
+The morphologic and immunohistochemical findings are diagnostic of melanoma. The 
+Breslow thickness of 1.8 mm places this tumor in the T2 category (AJCC 8th edition).
+Sentinel lymph node biopsy is recommended for staging. BRAF mutation testing may be 
+considered for treatment planning. Close clinical follow-up is recommended.
+```
+
+---
+
+## Signature
+
+**Pathologist:**  
+[Name, MD]  
+[Board Certification]  
+[License number]
+
+**Electronically signed:** [Date and time]
+
+**Gross examination by:** [Name, credentials]  
+**Microscopic examination by:** [Name, MD]
+
+---
+
+## Template Notes for Different Specimen Types
+
+### Breast Biopsy
+
+**Key Elements:**
+- Histologic type (invasive ductal, lobular, etc.)
+- Nottingham grade (tubule formation, nuclear grade, mitotic count)
+- Size of invasive component
+- DCIS if present (grade, extent)
+- ER/PR/HER2 status
+- Margins for all components
+- Lymph nodes if present
+
+### Colon Resection
+
+**Key Elements:**
+- Tumor site and size
+- Histologic type and grade
+- Depth of invasion (T stage)
+- Lymph nodes (number positive/total examined)
+- Margins (proximal, distal, radial/circumferential)
+- Lymphovascular and perineural invasion
+- Tumor deposits
+- MSI/MMR status
+
+### Prostate Biopsy/Resection
+
+**Key Elements:**
+- Gleason score (pattern 1 + pattern 2 = total)
+- Grade group (1-5)
+- Percent involvement per core/specimen
+- Extraprostatic extension (if radical prostatectomy)
+- Seminal vesicle invasion
+- Margins
+- Perineural invasion
+
+---
+
+## Frozen Section Report (if applicable)
+
+**Frozen Section Diagnosis:**
+
+**Specimen:** [Description]  
+**Clinical Question:** [Reason for frozen]  
+**Frozen Section Diagnosis:** [Diagnosis given intraoperatively]  
+**Time:** [Time reported]  
+**Pathologist:** [Name]
+
+**Note:** Permanent sections to follow.
+
+**Final Diagnosis:** [State if concordant or discordant with frozen]
+
+