How to Study Pathology in 2nd Year BHMS

from reportlab.lib.pagesizes import A4
from reportlab.lib import colors
from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
from reportlab.lib.units import cm, mm
from reportlab.platypus import (
    SimpleDocTemplate, Paragraph, Spacer, Table, TableStyle,
    HRFlowable, PageBreak, KeepTogether
)
from reportlab.lib.enums import TA_LEFT, TA_CENTER, TA_JUSTIFY
from reportlab.platypus import ListFlowable, ListItem

OUTPUT = "/home/daytona/workspace/bhms-pathology/BHMS_Pathology_Mnemonics_Notes.pdf"

doc = SimpleDocTemplate(
    OUTPUT,
    pagesize=A4,
    rightMargin=2*cm, leftMargin=2*cm,
    topMargin=2.2*cm, bottomMargin=2.2*cm,
    title="BHMS 2nd Year General Pathology – Mnemonics & Notes",
    author="Orris"
)

W = A4[0] - 4*cm  # usable width

# ── Color palette ──────────────────────────────────────────────────────────────
C_DARK   = colors.HexColor("#1a2e44")   # deep navy
C_TEAL   = colors.HexColor("#0d7377")   # teal accent
C_GOLD   = colors.HexColor("#f0a500")   # gold highlight
C_MINT   = colors.HexColor("#e8f8f5")   # light mint bg
C_CREAM  = colors.HexColor("#fffbf0")   # cream bg
C_RED    = colors.HexColor("#c0392b")   # important/mnemonic red
C_PURPLE = colors.HexColor("#6c3483")   # miasm purple
C_LGREY  = colors.HexColor("#f4f6f9")   # table alt row

SS = getSampleStyleSheet()

def style(name, parent="Normal", **kw):
    return ParagraphStyle(name, parent=SS[parent], **kw)

# styles
sTitle   = style("sTitle",   "Title",  fontSize=22, textColor=C_DARK,
                 spaceAfter=4, spaceBefore=0, alignment=TA_CENTER,
                 fontName="Helvetica-Bold")
sSub     = style("sSub",     "Normal", fontSize=11, textColor=C_TEAL,
                 spaceAfter=6, alignment=TA_CENTER, fontName="Helvetica")
sH1      = style("sH1",      "Normal", fontSize=14, textColor=colors.white,
                 spaceBefore=14, spaceAfter=4, fontName="Helvetica-Bold",
                 leftIndent=0, backColor=C_DARK, borderPad=5)
sH2      = style("sH2",      "Normal", fontSize=12, textColor=C_TEAL,
                 spaceBefore=10, spaceAfter=3, fontName="Helvetica-Bold",
                 leftIndent=2)
sBody    = style("sBody",    "Normal", fontSize=9.5, leading=14,
                 spaceAfter=4, alignment=TA_JUSTIFY, textColor=colors.HexColor("#2c2c2c"))
sBullet  = style("sBullet",  "Normal", fontSize=9.5, leading=13,
                 leftIndent=14, firstLineIndent=-10, spaceAfter=2,
                 textColor=colors.HexColor("#2c2c2c"))
sMnem    = style("sMnem",    "Normal", fontSize=10.5, leading=15,
                 textColor=C_RED, fontName="Helvetica-Bold",
                 spaceBefore=4, spaceAfter=2)
sMnemExp = style("sMnemExp", "Normal", fontSize=9.5, leading=13,
                 leftIndent=14, textColor=colors.HexColor("#5d0b0b"), spaceAfter=4)
sMiasm   = style("sMiasm",   "Normal", fontSize=9.5, leading=13,
                 textColor=C_PURPLE, fontName="Helvetica-BoldOblique",
                 spaceBefore=3, spaceAfter=5)
sKP      = style("sKP",      "Normal", fontSize=9.5, leading=13,
                 leftIndent=14, firstLineIndent=-10, spaceAfter=2,
                 textColor=colors.HexColor("#1a4a1a"))
sNote    = style("sNote",    "Normal", fontSize=8.8, leading=12,
                 textColor=colors.HexColor("#555555"), leftIndent=8,
                 fontName="Helvetica-Oblique", spaceAfter=6)
sFooter  = style("sFooter",  "Normal", fontSize=8, textColor=colors.grey,
                 alignment=TA_CENTER)

def h1(text):
    return [
        Spacer(1, 4),
        Paragraph(f"  {text}", sH1),
        Spacer(1, 2),
    ]

def h2(text):
    return [Paragraph(text, sH2)]

def body(text):
    return [Paragraph(text, sBody)]

def bullet(items, symbol="•"):
    return [Paragraph(f"{symbol}  {it}", sBullet) for it in items]

def mnemonic(label, expansion, tip=""):
    out = [Paragraph(f"🧠  {label}", sMnem),
           Paragraph(expansion, sMnemExp)]
    if tip:
        out.append(Paragraph(f"💡 {tip}", sNote))
    return out

def miasm(text):
    return [Paragraph(f"☯  Miasmatic Note: {text}", sMiasm)]

def keypoint(items):
    return [Paragraph(f"★  {it}", sKP) for it in items]

def hr():
    return [HRFlowable(width="100%", thickness=0.5, color=colors.HexColor("#cccccc"), spaceAfter=4, spaceBefore=2)]

def box_table(rows, header=None, col_widths=None):
    """Generic 2-column comparison table."""
    data = []
    if header:
        data.append(header)
    data.extend(rows)
    if col_widths is None:
        col_widths = [W*0.45, W*0.55]
    ts = TableStyle([
        ("BACKGROUND",   (0,0), (-1,0), C_DARK),
        ("TEXTCOLOR",    (0,0), (-1,0), colors.white),
        ("FONTNAME",     (0,0), (-1,0), "Helvetica-Bold"),
        ("FONTSIZE",     (0,0), (-1,-1), 9),
        ("ROWBACKGROUNDS",(0,1),(-1,-1), [C_CREAM, C_MINT]),
        ("GRID",         (0,0), (-1,-1), 0.4, colors.HexColor("#bbbbbb")),
        ("VALIGN",       (0,0), (-1,-1), "TOP"),
        ("LEFTPADDING",  (0,0), (-1,-1), 6),
        ("RIGHTPADDING", (0,0), (-1,-1), 6),
        ("TOPPADDING",   (0,0), (-1,-1), 4),
        ("BOTTOMPADDING",(0,0), (-1,-1), 4),
    ])
    if not header:
        ts.add("BACKGROUND", (0,0), (-1,0), C_MINT)
        ts.add("TEXTCOLOR",  (0,0), (-1,0), C_DARK)
    t = Table(data, colWidths=col_widths, style=ts, hAlign="LEFT")
    return [t, Spacer(1, 6)]

# ══════════════════════════════════════════════════════════════════════════════
# BUILD CONTENT
# ══════════════════════════════════════════════════════════════════════════════
story = []

# ── COVER ──────────────────────────────────────────────────────────────────────
story.append(Spacer(1, 2*cm))
story.append(Paragraph("BHMS 2nd Year", sSub))
story.append(Paragraph("General Pathology", sTitle))
story.append(Paragraph("Mnemonics & Quick Notes", sTitle))
story.append(Spacer(1, 6))
story.append(HRFlowable(width="80%", thickness=2, color=C_GOLD, hAlign="CENTER"))
story.append(Spacer(1, 8))
story.append(Paragraph("Covering all CCIM syllabus topics · Robbins-based · With Miasmatic Correlations", sSub))
story.append(Spacer(1, 1.5*cm))

toc_items = [
    "1. Introduction to Pathology",
    "2. Cell Injury & Cellular Adaptations",
    "3. Necrosis & Apoptosis",
    "4. Inflammation (Acute & Chronic)",
    "5. Mediators of Inflammation",
    "6. Tissue Repair & Wound Healing",
    "7. Immunity & Hypersensitivity",
    "8. Neoplasia",
    "9. Haemodynamic Disorders (Thrombosis, Embolism, Oedema, Shock)",
    "10. Degeneration, Amyloidosis & Pigmentation Disorders",
    "11. Miscellaneous (Gangrene, Infarction, Pyrexia, Infection)",
]
toc_data = [[Paragraph("TABLE OF CONTENTS", style("tocH","Normal",fontSize=10,
             fontName="Helvetica-Bold", textColor=colors.white))]]
for item in toc_items:
    toc_data.append([Paragraph(item, style("tocI","Normal",fontSize=9,textColor=C_DARK,leading=14))])
toc_ts = TableStyle([
    ("BACKGROUND",  (0,0), (-1,0), C_DARK),
    ("BACKGROUND",  (0,1), (-1,-1), C_CREAM),
    ("GRID",        (0,0), (-1,-1), 0.3, colors.HexColor("#cccccc")),
    ("LEFTPADDING", (0,0), (-1,-1), 10),
    ("TOPPADDING",  (0,0), (-1,-1), 5),
    ("BOTTOMPADDING",(0,0),(-1,-1), 5),
])
story.append(Table(toc_data, colWidths=[W*0.75], style=toc_ts, hAlign="CENTER"))
story.append(PageBreak())

# ══════════════════════════════════════════════════════════════════════════════
# 1. INTRODUCTION TO PATHOLOGY
# ══════════════════════════════════════════════════════════════════════════════
story += h1("1. INTRODUCTION TO PATHOLOGY")
story += body("Pathology is the scientific study of <b>structural and functional changes</b> in cells, tissues, and organs that underlie disease. It bridges basic sciences and clinical medicine.")
story += h2("Four Aspects of a Disease (CAMP)")
story += mnemonic("CAMP",
    "C – Cause (Aetiology)\nA – Abnormal cell/tissue changes (Morphology)\nM – Mechanism (Pathogenesis)\nP – Physiological/functional consequences (Clinical significance)",
    "Every time you study a disease, answer these 4 questions.")
story += h2("Types of Pathology")
story += bullet([
    "<b>General Pathology:</b> Reactions of cells to abnormal stimuli (applies to all diseases)",
    "<b>Systemic/Special Pathology:</b> Disease processes in specific organs or systems",
    "<b>Clinical Pathology:</b> Lab-based diagnosis (haematology, biochemistry, microbiology)",
])
story += miasm("Psora = functional/disturbed reactions; Sycosis = excess/overgrowth; Syphilis = destruction/necrosis. All pathological processes can be mapped to these.")
story += hr()

# ══════════════════════════════════════════════════════════════════════════════
# 2. CELL INJURY & ADAPTATIONS
# ══════════════════════════════════════════════════════════════════════════════
story += h1("2. CELL INJURY &amp; CELLULAR ADAPTATIONS")
story += h2("Causes of Cell Injury")
story += mnemonic("HITTING",
    "H – Hypoxia / Ischaemia\nI – Immunologic reactions\nT – Toxins &amp; Drugs\nT – Trauma / Physical agents\nI – Infection (micro-organisms)\nN – Nutritional imbalances\nG – Genetic defects",
    "The 7 major causes of cell injury from Robbins Ch.1")
story += h2("Cellular Adaptations (HAMHA)")
story += mnemonic("HAMHA",
    "H – Hypertrophy (↑ cell size)\nA – Atrophy (↓ cell size)\nM – Metaplasia (one cell type → another)\nH – Hyperplasia (↑ cell number)\nA – Anaplasia (loss of differentiation – seen in malignancy)",
    "Reversible adaptations except anaplasia. Know the stimulus for each.")
story += h2("Reversible vs. Irreversible Cell Injury")
story += box_table(
    [
        [Paragraph("<b>Feature</b>", sBody), Paragraph("<b>Reversible</b>", sBody), Paragraph("<b>Irreversible</b>", sBody)],
        ["Cellular swelling", "Yes", "Yes → blebbing"],
        ["Mitochondria", "Swelling only", "Densities + rupture"],
        ["Plasma membrane", "Intact", "Disrupted"],
        ["DNA", "Normal", "Fragmentation"],
        ["Lysosomes", "Intact", "Ruptured"],
        ["Outcome", "Recovery if cause removed", "Cell death (necrosis/apoptosis)"],
    ],
    col_widths=[W*0.28, W*0.36, W*0.36],
    header=None
)
story += h2("Key Mechanisms of Irreversible Injury (DOMED)")
story += mnemonic("DOMED",
    "D – DNA damage\nO – Oxidative stress (free radicals)\nM – Mitochondrial dysfunction\nE – ER stress / misfolded proteins\nD – Disruption of membrane (calcium influx)",
    "These 5 mechanisms converge to cause cell death in most serious injuries.")
story += keypoint([
    "Calcium influx is the FINAL COMMON PATHWAY of cell injury leading to irreversible damage",
    "Free radicals cause injury by lipid peroxidation, protein cross-linking, and DNA breaks",
    "ER stress triggers the Unfolded Protein Response (UPR) – if overwhelmed → apoptosis",
])
story += miasm("Hypoxic cell injury (ischaemia) represents the acute Syphilitic destructive process at the cellular level.")
story += hr()

# ══════════════════════════════════════════════════════════════════════════════
# 3. NECROSIS & APOPTOSIS
# ══════════════════════════════════════════════════════════════════════════════
story += h1("3. NECROSIS &amp; APOPTOSIS")
story += h2("Types of Necrosis (CALF-CG)")
story += mnemonic("CALF-CG",
    "C – Coagulative necrosis (most common; all organs EXCEPT brain; e.g., MI)\nA – Aseptic liquefactive = liquefactive (brain, abscess)\nL – Liquefactive necrosis (bacterial infection, brain infarct)\nF – Fat necrosis (pancreas, breast trauma – chalky white deposits)\nC – Caseous necrosis (TB – cheese-like; soft, crumbly)\nG – Gangrenous necrosis (limbs; dry/wet/gas types)",
    "Add Fibrinoid necrosis (immune complex deposition in vessel walls) as the 7th type.")
story += box_table(
    [
        [Paragraph("<b>Type</b>", sBody), Paragraph("<b>Example/Cause</b>", sBody), Paragraph("<b>Microscopy</b>", sBody)],
        ["Coagulative",  "Myocardial infarction",        "Ghost outlines of cells preserved"],
        ["Liquefactive", "Brain infarct, abscess",        "Liquefied centre, pus cells"],
        ["Caseous",      "Tuberculosis",                  "Amorphous granular material + giant cells"],
        ["Fat",          "Acute pancreatitis",            "Saponification – chalky white areas"],
        ["Fibrinoid",    "Vasculitis, malignant HTN",     "Pink homogeneous vessel wall"],
        ["Gangrenous",   "Limb ischaemia, diabetes",      "Dry: coagulative; Wet: liquefactive mixed"],
    ],
    col_widths=[W*0.22, W*0.38, W*0.40],
    header=None
)
story += h2("Apoptosis vs. Necrosis")
story += box_table(
    rows=[
        [Paragraph("<b>Feature</b>", sBody), Paragraph("<b>Apoptosis</b>", sBody), Paragraph("<b>Necrosis</b>", sBody)],
        ["Cell size",     "Shrinks",              "Swells"],
        ["Nucleus",       "Pyknosis → karyorrhexis", "Karyolysis"],
        ["Membrane",      "Intact (blebbing)",    "Disrupted"],
        ["Inflammation",  "None",                 "Present"],
        ["Initiators",    "Caspases",             "No caspases"],
        ["Energy (ATP)",  "Required",             "Not required"],
        ["Pathological?", "Can be normal (e.g., embryogenesis, immune cells)", "Always pathological"],
    ],
    col_widths=[W*0.25, W*0.37, W*0.38],
    header=None
)
story += mnemonic("Apoptosis = A.P.O.P.T.O.S.I.S",
    "A – Absent inflammation\nP – Programmed\nO – Orderly\nP – Pyknotic nucleus\nT – Tiny (cell shrinks)\nO – Own machinery (caspases)\nS – Safe (membrane intact)\nI – Individual cells\nS – Signal-mediated",
    "Contrasts with NECROSIS which is disorderly, inflammatory, and involves groups of cells.")
story += keypoint([
    "Apoptosis: intrinsic pathway (mitochondria, Bcl-2 family) + extrinsic pathway (death receptors Fas/TNF-R)",
    "Caspase-3 is the EXECUTIONER caspase – final common pathway of apoptosis",
    "Nuclear changes: Pyknosis (condensation) → Karyorrhexis (fragmentation) → Karyolysis (dissolution)",
])
story += miasm("Necrosis → Syphilitic miasm (destructive). Uncontrolled apoptosis in chronic disease → also Syphilitic. Excess cell proliferation (failure of apoptosis) → Sycotic miasm.")
story += hr()

# ══════════════════════════════════════════════════════════════════════════════
# 4. INFLAMMATION
# ══════════════════════════════════════════════════════════════════════════════
story += h1("4. INFLAMMATION")
story += h2("Cardinal Signs of Acute Inflammation")
story += mnemonic("PRISH",
    "P – Pain (Dolor)\nR – Redness (Rubor)\nI – (i)mmobility / Loss of function (Functio laesa)\nS – Swelling (Tumor)\nH – Heat (Calor)",
    "Classic 5 cardinal signs. Celsus described first 4; Virchow added the 5th (loss of function).")
story += h2("Vascular Events in Acute Inflammation (VIVID)")
story += mnemonic("VIVID",
    "V – Vasodilatation (arterioles dilate → ↑ blood flow → redness &amp; heat)\nI – Increased vascular permeability (gaps between endothelial cells)\nV – Vascular stasis (blood slows down → leukocytes marginate)\nI – Interstitial fluid increases (oedema / exudate)\nD – Diapedesis (leukocytes migrate through vessel wall)",
    "Sequence: transient vasoconstriction → vasodilation → increased permeability → stasis → cell emigration")
story += h2("Steps of Leukocyte Recruitment (MARBLE)")
story += mnemonic("MARBLE",
    "M – Margination (leukocytes move to periphery of vessel)\nA – Adhesion/Rolling (selectins: P-selectin, E-selectin)\nR – Rolling to firm Adhesion (integrins: ICAM-1, VCAM-1)\nB – Beyond (transmigration / diapedesis through vessel wall)\nL – Locomotion (chemotaxis toward stimulus)\nE – Engulfment (phagocytosis + killing)",
    "Deficiency of CD18 (LFA-1 integrin) = Leukocyte Adhesion Deficiency – recurrent bacterial infections.")
story += h2("Exudate vs. Transudate")
story += box_table(
    rows=[
        [Paragraph("<b>Feature</b>", sBody), Paragraph("<b>Exudate</b>", sBody), Paragraph("<b>Transudate</b>", sBody)],
        ["Cause",       "Inflammation",             "Hydrostatic/osmotic imbalance"],
        ["Protein",     "High (>3g/dL)",            "Low (<3g/dL)"],
        ["Specific gravity", ">1.020",              "<1.012"],
        ["Cells",       "Many WBCs",                "Few cells"],
        ["Colour",      "Turbid",                   "Clear"],
        ["Example",     "Pneumonia, empyema",        "CCF, nephrotic syndrome"],
    ],
    col_widths=[W*0.28, W*0.36, W*0.36],
    header=None
)
story += h2("Morphological Types of Acute Inflammation (SFPU)")
story += mnemonic("SFPU",
    "S – Serous (watery; e.g., blisters, pleural effusion)\nF – Fibrinous (fibrin-rich; e.g., pericarditis – 'bread &amp; butter')\nP – Purulent/Suppurative (pus = neutrophils + necrotic debris; abscess)\nU – Ulcerative (surface epithelium lost; e.g., peptic ulcer)",
    "Know the example for each type – examiners love asking these.")
story += h2("Chronic Inflammation")
story += bullet([
    "<b>Definition:</b> Inflammation of prolonged duration (weeks–months) with simultaneous active injury and healing",
    "<b>Cells:</b> Macrophages (dominant), lymphocytes, plasma cells, eosinophils, mast cells, fibroblasts",
    "<b>Causes:</b> Persistent infection (TB, syphilis), autoimmune disease, prolonged chemical/foreign body exposure",
    "<b>Granulomatous inflammation:</b> Specialised chronic inflammation; central necrosis surrounded by macrophages (epithelioid) + Langhans giant cells + lymphocytes",
])
story += mnemonic("Granuloma causes – SAINT",
    "S – Sarcoidosis (non-caseating)\nA – Actinomycosis\nI – Infection (TB – caseating; Leprosy)\nN – Neoplasm (Hodgkin lymphoma)\nT – Talc / Foreign body",
    "TB granuloma = caseating; Sarcoid = non-caseating. Key exam distinction.")
story += miasm("Acute inflammation = Psoric reaction (first-line defence). Chronic inflammation with tissue destruction = Syphilitic. Granuloma formation (encapsulation) = Sycotic.")
story += hr()

# ══════════════════════════════════════════════════════════════════════════════
# 5. MEDIATORS OF INFLAMMATION
# ══════════════════════════════════════════════════════════════════════════════
story += h1("5. MEDIATORS OF INFLAMMATION")
story += mnemonic("CHIPS-KC",
    "C – Complement (C3a, C5a – chemotaxis, opsonisation, MAC)\nH – Histamine (mast cells/platelets – immediate vascular permeability)\nI – IL-1 &amp; IL-6 (fever, acute phase response)\nP – Prostaglandins (vasodilation, pain, fever)\nS – Serotonin (platelets – vascular permeability)\nK – Kinins (bradykinin – pain, vasodilation)\nC – Cytokines (TNF, chemokines – leukocyte recruitment)",
    "Source, action, and pharmacology (NSAIDs block COX → prostaglandins; steroids block phospholipase A2).")
story += box_table(
    rows=[
        [Paragraph("<b>Mediator</b>", sBody), Paragraph("<b>Source</b>", sBody), Paragraph("<b>Key Action</b>", sBody)],
        ["Histamine",     "Mast cells, basophils, platelets",    "↑ Permeability (early, immediate)"],
        ["Prostaglandins","Arachidonic acid via COX",            "Vasodilation, pain, fever"],
        ["Leukotrienes",  "Arachidonic acid via LOX",            "Bronchoconstriction, ↑ permeability"],
        ["C3a &amp; C5a", "Complement cascade",                  "Chemotaxis, anaphylatoxin (histamine release)"],
        ["TNF-α",         "Macrophages, T cells, mast cells",    "Endothelial activation, fever, cachexia"],
        ["IL-1",          "Macrophages, endothelium, epithelium","Fever (hypothalamic), acute phase response"],
        ["Bradykinin",    "Plasma kininogens",                   "Pain, vasodilation, ↑ permeability"],
        ["PAF",           "Mast cells, neutrophils",             "Platelet aggregation, bronchoconstriction"],
    ],
    col_widths=[W*0.25, W*0.37, W*0.38],
    header=None
)
story += keypoint([
    "NSAIDs (aspirin, ibuprofen) block COX → inhibit prostaglandins (anti-inflammatory, antipyretic, analgesic)",
    "Corticosteroids block phospholipase A2 → inhibit BOTH prostaglandins AND leukotrienes",
    "C5a = most powerful chemotactic factor from complement; also an anaphylatoxin",
    "Arachidonic acid: COX pathway → prostaglandins (PGE2, PGI2) + thromboxane; LOX pathway → leukotrienes",
])
story += hr()

# ══════════════════════════════════════════════════════════════════════════════
# 6. TISSUE REPAIR & WOUND HEALING
# ══════════════════════════════════════════════════════════════════════════════
story += h1("6. TISSUE REPAIR &amp; WOUND HEALING")
story += h2("Types of Cells by Regenerative Ability")
story += mnemonic("LABILE-STABLE-PERMANENT",
    "LABILE cells – divide continuously (always in cell cycle)\n   → Epidermis, GI epithelium, bone marrow, lymphoid tissue\nSTABLE cells – quiescent; can re-enter cell cycle when stimulated\n   → Liver, kidney tubules, smooth muscle, fibroblasts\nPERMANENT cells – cannot regenerate (terminally differentiated)\n   → Neurons, cardiac muscle cells, skeletal muscle cells (minimal)",
    "Liver is STABLE → it can regenerate after partial hepatectomy (up to 70% resection).")
story += h2("Steps of Wound Healing (IRON-FIRM)")
story += mnemonic("IRON-FIRM",
    "I – Inflammation (first 24-48 hrs; neutrophils clean wound)\nR – Re-epithelialization (epidermis migrates from edges)\nO – Organise (granulation tissue forms: angiogenesis + fibroblasts)\nN – New vessels (angiogenesis driven by VEGF)\nF – Fibroplasia (fibroblasts proliferate, deposit collagen)\nI – Integration (collagen matures; type III → type I)\nR – Remodelling (MMP enzymes remodel matrix; scar contracts)\nM – Max strength (scar reaches 70-80% original strength by 3 months)",
    "Granulation tissue = new capillaries + fibroblasts + macrophages. NOT same as granuloma.")
story += h2("Healing by Primary vs. Secondary Intention")
story += box_table(
    rows=[
        [Paragraph("<b>Feature</b>", sBody), Paragraph("<b>Primary Intention</b>", sBody), Paragraph("<b>Secondary Intention</b>", sBody)],
        ["Wound edges",    "Approximated (sutured)",         "Widely separated, open"],
        ["Tissue loss",    "Minimal",                        "Significant"],
        ["Granulation tissue","Little",                      "Abundant"],
        ["Scar",           "Thin, neat",                     "Large, broad"],
        ["Contraction",    "Minimal",                        "Significant (myofibroblasts)"],
        ["Example",        "Surgical incision",              "Chronic ulcer, abscess cavity"],
    ],
    col_widths=[W*0.25, W*0.37, W*0.38],
    header=None
)
story += h2("Factors Impairing Wound Healing (DIVAS)")
story += mnemonic("DIVAS",
    "D – Diabetes mellitus (poor vascularity, immune dysfunction)\nI – Infection (prolongs inflammation)\nV – Vitamin deficiency (Vit C: collagen synthesis; Vit A: re-epithelialization; Zinc: enzyme cofactors)\nA – Anaemia / Inadequate blood supply\nS – Steroids (suppress inflammation, inhibit fibroplasia)",
    "Foreign body, malnutrition, and old age are also important factors.")
story += miasm("Repair and regeneration = Psoric tendency (the healthy restoring tendency). Excessive scar / keloid = Sycotic (hyper-proliferative). Chronic non-healing wound = Syphilitic.")
story += hr()

# ══════════════════════════════════════════════════════════════════════════════
# 7. IMMUNITY & HYPERSENSITIVITY
# ══════════════════════════════════════════════════════════════════════════════
story += h1("7. IMMUNITY &amp; HYPERSENSITIVITY")
story += h2("Types of Hypersensitivity (ACID)")
story += mnemonic("ACID",
    "A – Anaphylactic / Immediate (Type I) – IgE mediated\nC – Cytotoxic (Type II) – IgG/IgM vs. cell-surface antigens\nI – Immune-complex (Type III) – Ag-Ab complexes deposited in tissues\nD – Delayed-type / Cell-mediated (Type IV) – T-cell mediated",
    "Types I, II, III are antibody-mediated (humoral). Type IV is T-cell mediated (cellular).")
story += box_table(
    rows=[
        [Paragraph("<b>Type</b>", sBody), Paragraph("<b>Mechanism</b>", sBody), Paragraph("<b>Example</b>", sBody)],
        ["I – Anaphylactic",    "IgE on mast cells → degranulation",              "Allergic rhinitis, asthma, anaphylaxis, urticaria"],
        ["II – Cytotoxic",      "IgG/IgM + complement → cell lysis",              "Autoimmune haemolytic anaemia, transfusion reaction, Graves disease"],
        ["III – Immune complex","Ag-Ab complexes → complement → inflammation",     "SLE, post-streptococcal GN, serum sickness, Arthus reaction"],
        ["IV – Delayed (DTH)",  "Sensitized T-cells (CD4/CD8) → macrophage activ.","TB (Mantoux), contact dermatitis, graft rejection"],
    ],
    col_widths=[W*0.22, W*0.40, W*0.38],
    header=None
)
story += keypoint([
    "Type I: Sensitization (1st exposure) → IgE formed → binds mast cell Fc receptors. 2nd exposure → cross-linking → degranulation",
    "Type III: Deposited in kidney glomeruli (GN), joints (arthritis), blood vessels (vasculitis) → LOW complement levels",
    "Type IV: ONLY type NOT antibody mediated. NO complement. Takes 48-72 hrs (hence 'delayed')",
    "SLE is a mix of Type II and Type III hypersensitivity",
])
story += miasm("Hypersensitivity disorders = Psoric (functional, reactive). Autoimmune destruction = Syphilitic. Chronic fibrosing conditions from immune reactions = Sycotic.")
story += hr()

# ══════════════════════════════════════════════════════════════════════════════
# 8. NEOPLASIA
# ══════════════════════════════════════════════════════════════════════════════
story += h1("8. NEOPLASIA")
story += h2("Benign vs. Malignant Tumours (DISC-MEND)")
story += mnemonic("BENIGN vs. MALIGNANT – 7 Differences (DICES)",
    "D – Differentiation (Benign: well-differentiated; Malignant: poorly/anaplastic)\nI – Invasion (Benign: no invasion; Malignant: invades locally)\nC – Capsule (Benign: encapsulated; Malignant: not encapsulated)\nE – Edges (Benign: smooth; Malignant: irregular)\nS – Spread / Metastasis (Benign: NEVER metastasizes; Malignant: DOES)",
    "Rate of growth: Benign = slow; Malignant = rapid. Necrosis: only in malignant.")
story += h2("Tumour Nomenclature")
story += box_table(
    rows=[
        [Paragraph("<b>Cell of Origin</b>", sBody), Paragraph("<b>Benign</b>", sBody), Paragraph("<b>Malignant</b>", sBody)],
        ["Epithelial (glandular)",   "Adenoma",          "Adenocarcinoma"],
        ["Epithelial (squamous)",    "Papilloma",        "Squamous cell carcinoma"],
        ["Connective tissue (fat)",  "Lipoma",           "Liposarcoma"],
        ["Connective tissue (bone)", "Osteoma",          "Osteosarcoma"],
        ["Smooth muscle",           "Leiomyoma",        "Leiomyosarcoma"],
        ["Blood vessels",           "Haemangioma",      "Angiosarcoma"],
        ["Lymphoid tissue",         "—",                "Lymphoma / Leukaemia"],
        ["Melanocytes",             "Naevus (mole)",    "Melanoma"],
    ],
    col_widths=[W*0.35, W*0.30, W*0.35],
    header=None
)
story += h2("Hallmarks of Cancer (SASH-AEIR)")
story += mnemonic("SASH-AEIR (8 Hallmarks – Hanahan &amp; Weinberg)",
    "S – Self-sufficiency in growth signals (oncogene activation)\nA – Avoiding apoptosis\nS – Sustained angiogenesis (VEGF)\nH – HanAhling immune destruction\nA – Activating invasion and metastasis\nE – Evading growth suppressors (p53, Rb mutation)\nI – Inducing genomic instability &amp; mutation\nR – Replicative immortality (telomerase activation)",
    "Two enabling characteristics: tumour-promoting inflammation + deregulating cellular energetics.")
story += h2("Routes of Metastasis (SLID)")
story += mnemonic("SLID",
    "S – Seeding of body cavities (e.g., ovarian → peritoneum)\nL – Lymphatic spread (most common for CARCINOMAS)\nI – Implantation / Direct extension (rare, iatrogenic)\nD – Direct blood-borne (Haematogenous – most common for SARCOMAS)",
    "Carcinomas → lymphatics first. Sarcomas → blood vessels first. Brain mets: lung &gt; breast &gt; kidney &gt; melanoma.")
story += keypoint([
    "Oncogenes (accelerators): RAS, MYC, HER2/neu – gain of function mutations",
    "Tumour suppressor genes (brakes): TP53 (guardian of genome), RB (retinoblastoma) – loss of function",
    "p53 is the MOST COMMONLY mutated gene in human cancers",
    "Carcinogenesis stages: Initiation → Promotion → Progression",
    "Chemical carcinogens: aflatoxin (liver), asbestos (mesothelioma), benzene (leukaemia), aniline dye (bladder)",
])
story += miasm("Neoplasia = quintessential Sycotic miasm (uncontrolled growth, excess cell proliferation). Tumour necrosis + invasion = Syphilitic overlay.")
story += hr()

# ══════════════════════════════════════════════════════════════════════════════
# 9. HAEMODYNAMIC DISORDERS
# ══════════════════════════════════════════════════════════════════════════════
story += h1("9. HAEMODYNAMIC DISORDERS")

story += h2("Virchow's Triad (Thrombosis)")
story += mnemonic("EHS",
    "E – Endothelial injury (most important; e.g., atherosclerosis, hypertension)\nH – Haemodynamic disturbance (stasis or turbulence; e.g., atrial fibrillation, DVT)\nS – Hypercoagulability of blood (inherited: Factor V Leiden; acquired: pregnancy, malignancy)",
    "Remember: all 3 elements identified by Rudolf Virchow in 1856. At least one is present in every thrombosis.")
story += h2("Types of Embolism")
story += mnemonic("FAT BAG",
    "F – Fat embolism (long bone fractures)\nA – Air/Gas embolism (surgery, IV lines, decompression sickness)\nT – Thrombo-embolism (most common! DVT → pulmonary embolism)\nB – Bacterial/Septic embolism (infective endocarditis)\nA – Amniotic fluid embolism (obstetric emergency)\nG – Gaseous embolism (nitrogen – caisson disease / the bends)",
    "Pulmonary thromboembolism is the MOST COMMON type; originates from deep veins of leg (DVT).")
story += h2("Types of Shock (COHN-S)")
story += mnemonic("COHN-S",
    "C – Cardiogenic (pump failure: MI, cardiac tamponade)\nO – Obstructive (outflow obstruction: PE, tension pneumothorax)\nH – Hypovolaemic (blood/fluid loss: haemorrhage, burns, diarrhoea)\nN – Neurogenic (loss of vasomotor tone: spinal injury)\nS – Septic/Distributive (bacterial toxins → widespread vasodilation)",
    "All types end in: ↓ cardiac output → ↓ tissue perfusion → multi-organ failure.")
story += h2("Oedema Mechanisms (HOLI)")
story += mnemonic("HOLI",
    "H – Hydrostatic pressure ↑ (e.g., right heart failure → peripheral oedema)\nO – Oncotic (colloid osmotic) pressure ↓ (hypoalbuminaemia: nephrotic, cirrhosis, malnutrition)\nL – Lymphatic obstruction (lymphoedema: filariasis, post-mastectomy)\nI – Inflammation → ↑ vascular permeability (inflammatory oedema)",
    "Pulmonary oedema in LEFT heart failure; peripheral oedema in RIGHT heart failure.")
story += miasm("Thrombosis / vascular obstruction → Syphilitic (destructive, irreversible). Oedema/accumulations → Sycotic (excess fluid, retention).")
story += hr()

# ══════════════════════════════════════════════════════════════════════════════
# 10. DEGENERATION, AMYLOIDOSIS & PIGMENTATION
# ══════════════════════════════════════════════════════════════════════════════
story += h1("10. DEGENERATION, AMYLOIDOSIS &amp; PIGMENTATION")
story += h2("Types of Degeneration")
story += bullet([
    "<b>Cloudy swelling (hydropic degeneration):</b> Earliest reversible change; cell swells with water",
    "<b>Fatty change (steatosis):</b> Lipid accumulation in cell; seen in liver (alcohol, malnutrition), heart, kidney",
    "<b>Hyaline degeneration:</b> Homogeneous, glassy pink material (e.g., hyaline arteriolosclerosis, Mallory bodies in liver)",
    "<b>Mucinous degeneration:</b> Excess mucin; e.g., myxoedema, mucinous carcinoma",
    "<b>Amyloid degeneration:</b> Abnormal protein deposit in tissues",
])
story += h2("Amyloidosis – Key Facts")
story += mnemonic("AMYLOID",
    "A – Abnormal protein (beta-pleated sheet configuration)\nM – Multiple organs affected (kidney, heart, liver, spleen)\nY – Yellow-green birefringence with Congo Red stain under POLARISED light\nL – Low solubility (insoluble extracellular deposits)\nO – Often associated with chronic disease or plasma cell dyscrasias\nI – Immunoglobulin light chains (AL amyloid) OR SAA protein (AA amyloid)\nD – Diagnosis: Congo Red staining of biopsy",
    "Apple-green birefringence under polarised light with Congo Red = PATHOGNOMONIC of amyloid.")
story += box_table(
    rows=[
        [Paragraph("<b>Type</b>", sBody), Paragraph("<b>Precursor Protein</b>", sBody), Paragraph("<b>Associated Condition</b>", sBody)],
        ["AL amyloid",    "Immunoglobulin light chains",    "Multiple myeloma, primary amyloidosis"],
        ["AA amyloid",    "Serum amyloid A protein",        "Rheumatoid arthritis, TB, Crohn disease"],
        ["Aβ amyloid",    "Amyloid precursor protein (APP)","Alzheimer disease"],
        ["ATTR amyloid",  "Transthyretin (TTR)",            "Senile systemic / familial amyloidosis"],
    ],
    col_widths=[W*0.22, W*0.38, W*0.40],
    header=None
)
story += h2("Pigmentation Disorders")
story += box_table(
    rows=[
        [Paragraph("<b>Pigment</b>", sBody), Paragraph("<b>Type</b>", sBody), Paragraph("<b>Condition / Example</b>", sBody)],
        ["Melanin",    "Endogenous",  "↑: Addison disease, melanoma; ↓: Albinism, Vitiligo"],
        ["Haemosiderin","Endogenous", "Haemochromatosis (iron overload), haemolysis"],
        ["Bilirubin",  "Endogenous",  "Jaundice (pre/intra/post-hepatic)"],
        ["Lipofuscin", "Endogenous",  "'Wear and tear' pigment; brown atrophy in elderly hearts"],
        ["Carbon",     "Exogenous",   "Anthracosis (lung); coal worker's pneumoconiosis"],
        ["Tattoo ink", "Exogenous",   "Skin (persists in macrophages in dermis)"],
    ],
    col_widths=[W*0.22, W*0.22, W*0.56],
    header=None
)
story += hr()

# ══════════════════════════════════════════════════════════════════════════════
# 11. MISCELLANEOUS IMPORTANT TOPICS
# ══════════════════════════════════════════════════════════════════════════════
story += h1("11. MISCELLANEOUS – GANGRENE, INFARCTION, PYREXIA, INFECTION")
story += h2("Types of Gangrene")
story += box_table(
    rows=[
        [Paragraph("<b>Type</b>", sBody), Paragraph("<b>Features</b>", sBody), Paragraph("<b>Example</b>", sBody)],
        ["Dry gangrene",   "Coagulative necrosis; dry, mummified; clear line of demarcation; less infection", "Atherosclerosis, Buerger disease (limbs)"],
        ["Wet gangrene",   "Liquefactive; foul smell; no clear line; spreads rapidly; bacterial infection", "Bowel infarction, diabetes foot"],
        ["Gas gangrene",   "Wet + gas bubbles; caused by Clostridium perfringens; crepitus; life-threatening", "Contaminated wounds, post-op"],
    ],
    col_widths=[W*0.22, W*0.42, W*0.36],
    header=None
)
story += h2("Infarction")
story += bullet([
    "<b>Definition:</b> Area of ischaemic necrosis caused by occlusion of vascular supply (arterial or venous)",
    "<b>Red (haemorrhagic) infarct:</b> Loose tissues (lung, gut) or dual blood supply (liver) or venous occlusion",
    "<b>White (anaemic) infarct:</b> Solid organs with end-arterial supply (heart, spleen, kidney)",
    "<b>Septic infarct:</b> From infected thrombus/embolus → becomes abscess",
])
story += mnemonic("Infarct Colour – RAWW",
    "R – Red = venous occlusion / dual blood supply\nA – Anaemic (white) = arterial occlusion in solid organs\nW – Wet / Septic = infected\nW – Watershed infarcts = border zones between 2 arterial territories",
    "Myocardial infarction → white/pale infarct (coagulative necrosis). Brain infarct → red if haemorrhagic.")
story += h2("Pyrexia (Fever)")
story += bullet([
    "<b>Definition:</b> Regulated ↑ in body temperature above normal (>37.2°C oral / >37.8°C oral 'fever')",
    "<b>Pyrogens:</b> Exogenous (LPS, bacterial toxins) → stimulate monocytes/macrophages → endogenous pyrogens (IL-1, IL-6, TNF) → act on hypothalamus → ↑ prostaglandins (PGE2) → reset thermostat upwards",
    "<b>Antipyretic mechanism of aspirin/paracetamol:</b> Inhibit COX → ↓ PGE2 → lower set point",
])
story += h2("Infection vs. Inflammation")
story += bullet([
    "<b>Infection:</b> Invasion and multiplication of microorganisms in host tissues causing injury",
    "<b>Inflammation:</b> Tissue RESPONSE to infection or any injurious stimulus",
    "All infections cause inflammation, but not all inflammation is due to infection",
    "<b>Sepsis:</b> Life-threatening systemic dysregulated immune response to infection → SIRS → organ failure",
])
story += miasm("Infection/inflammation = primarily Psoric (the organism defending). Destruction of tissue during infection = Syphilitic overlay. Chronic persistent infection = Sycotic (organism persisting despite defence).")
story += hr()

# ══════════════════════════════════════════════════════════════════════════════
# QUICK REFERENCE – ALL MNEMONICS
# ══════════════════════════════════════════════════════════════════════════════
story += PageBreak()
story += h1("QUICK REFERENCE – ALL MNEMONICS AT A GLANCE")
all_mnemonics = [
    ("CAMP",        "Aspects of disease: Cause, Abnormal morphology, Mechanism, Pathophysiology"),
    ("HITTING",     "Causes of cell injury: Hypoxia, Immunologic, Toxins, Trauma, Infection, Nutrition, Genetics"),
    ("HAMHA",       "Cellular adaptations: Hypertrophy, Atrophy, Metaplasia, Hyperplasia, Anaplasia"),
    ("DOMED",       "Irreversible injury mechanisms: DNA, Oxidative stress, Mitochondria, ER stress, Disruption of membrane"),
    ("CALF-CG",     "Types of necrosis: Coagulative, Aseptic liquefactive, Liquefactive, Fat, Caseous, Gangrenous"),
    ("APOPTOSIS",   "Features of apoptosis: Absent inflam., Programmed, Orderly, Pyknosis, Tiny, Own machinery, Safe, Individual, Signal"),
    ("PRISH",       "Cardinal signs: Pain, Redness, Immobility, Swelling, Heat"),
    ("VIVID",       "Vascular events in inflammation: Vasodilation, ↑ permeability, Vascular stasis, Interstitial fluid, Diapedesis"),
    ("MARBLE",      "Leukocyte recruitment: Margination, Adhesion, Rolling→firm, Beyond (transmigration), Locomotion, Engulfment"),
    ("SFPU",        "Types of acute inflammation: Serous, Fibrinous, Purulent, Ulcerative"),
    ("SAINT",       "Granuloma causes: Sarcoidosis, Actinomycosis, Infection (TB), Neoplasm, Talc/Foreign body"),
    ("CHIPS-KC",    "Mediators: Complement, Histamine, IL-1/6, Prostaglandins, Serotonin, Kinins, Cytokines"),
    ("LABILE-STABLE-PERMANENT", "Cell types by regeneration: Labile (always dividing), Stable (quiescent), Permanent (non-dividing)"),
    ("IRON-FIRM",   "Steps of wound healing"),
    ("DIVAS",       "Factors impairing healing: Diabetes, Infection, Vitamins deficiency, Anaemia, Steroids"),
    ("ACID",        "Hypersensitivity types: Anaphylactic (I), Cytotoxic (II), Immune complex (III), Delayed (IV)"),
    ("DICES",       "Benign vs. Malignant: Differentiation, Invasion, Capsule, Edges, Spread"),
    ("SASH-AEIR",   "Hallmarks of cancer (Hanahan & Weinberg 8 hallmarks)"),
    ("FAT BAG",     "Types of embolism: Fat, Air, Thrombo, Bacterial, Amniotic fluid, Gas"),
    ("EHS",         "Virchow's triad: Endothelial injury, Haemodynamic disturbance, hypercoagulability (S)"),
    ("COHN-S",      "Types of shock: Cardiogenic, Obstructive, Hypovolaemic, Neurogenic, Septic"),
    ("HOLI",        "Oedema mechanisms: Hydrostatic ↑, Oncotic ↓, Lymphatic obstruction, Inflammation"),
    ("AMYLOID",     "Amyloid: Abnormal protein, Multiple organs, Yellow-green with Congo Red, Low solubility, Often chronic, Immunoglobulin/SAA, Diagnosis=biopsy"),
    ("RAWW",        "Infarct colour: Red=venous, Anaemic=arterial, Wet=infected, Watershed=border zone"),
]

mnem_table_data = [[
    Paragraph("<b>Mnemonic</b>", style("mth","Normal",fontSize=9,fontName="Helvetica-Bold",textColor=colors.white)),
    Paragraph("<b>Stands For</b>", style("mth","Normal",fontSize=9,fontName="Helvetica-Bold",textColor=colors.white)),
]]
for i, (m, exp) in enumerate(all_mnemonics):
    bg = C_CREAM if i % 2 == 0 else C_MINT
    mnem_table_data.append([
        Paragraph(f"<font color='#c0392b'><b>{m}</b></font>", style("mc","Normal",fontSize=9,fontName="Helvetica-Bold")),
        Paragraph(exp, style("me","Normal",fontSize=8.5,leading=12)),
    ])

mts = TableStyle([
    ("BACKGROUND",    (0,0), (-1,0), C_DARK),
    ("ROWBACKGROUNDS",(0,1), (-1,-1), [C_CREAM, C_MINT]),
    ("GRID",          (0,0), (-1,-1), 0.3, colors.HexColor("#cccccc")),
    ("VALIGN",        (0,0), (-1,-1), "TOP"),
    ("LEFTPADDING",   (0,0), (-1,-1), 6),
    ("RIGHTPADDING",  (0,0), (-1,-1), 6),
    ("TOPPADDING",    (0,0), (-1,-1), 4),
    ("BOTTOMPADDING", (0,0), (-1,-1), 4),
])
story.append(Table(mnem_table_data, colWidths=[W*0.25, W*0.75], style=mts, hAlign="LEFT"))

# ── FOOTER PAGE ──────────────────────────────────────────────────────────────
story.append(PageBreak())
story.append(Spacer(1, 3*cm))
story.append(HRFlowable(width="80%", thickness=2, color=C_GOLD, hAlign="CENTER"))
story.append(Spacer(1, 10))
story.append(Paragraph("BHMS 2nd Year – General Pathology Mnemonics &amp; Notes", 
             style("fc","Normal",fontSize=13,fontName="Helvetica-Bold",textColor=C_DARK,alignment=TA_CENTER)))
story.append(Spacer(1, 6))
story.append(Paragraph("Based on: Robbins &amp; Kumar Basic Pathology | CCIM BHMS Syllabus", 
             style("fc2","Normal",fontSize=9,textColor=colors.grey,alignment=TA_CENTER)))
story.append(Spacer(1, 6))
story.append(Paragraph("Study Tip: Read Robbins for concepts → Use Harsh Mohan for exam answers → End each topic with miasmatic correlation.",
             style("fc3","Normal",fontSize=9,textColor=C_TEAL,alignment=TA_CENTER,fontName="Helvetica-Oblique")))
story.append(Spacer(1, 20))
story.append(HRFlowable(width="80%", thickness=0.5, color=colors.HexColor("#cccccc"), hAlign="CENTER"))

# ── BUILD ────────────────────────────────────────────────────────────────────
def add_page_number(canvas, doc):
    canvas.saveState()
    canvas.setFont("Helvetica", 8)
    canvas.setFillColor(colors.grey)
    canvas.drawString(2*cm, 1.2*cm, "BHMS 2nd Year | General Pathology Mnemonics & Notes")
    canvas.drawRightString(A4[0]-2*cm, 1.2*cm, f"Page {doc.page}")
    canvas.restoreState()

doc.build(story, onFirstPage=add_page_number, onLaterPages=add_page_number)
print(f"PDF created: {OUTPUT}")

Successfully replaced 1 instance(s) of the string in '/home/daytona/workspace/bhms-pathology/generate_pathology_notes.py'