cd /home/daytona/workspace && python -m markitdown "/home/daytona/workspace/atta…

cd /home/daytona/workspace && python -m markitdown "/home/daytona/workspace/atta…

cd /home/daytona/workspace && python3 -c " from pptx import Presentation import …

cd /home/daytona/workspace && python3 -c " import fitz # PyMuPDF doc = fitz.ope…

which node && node --version && ls /home/daytona/skills/pptx/

# Try extracting PDF text with pdftotext pdftotext "/home/daytona/workspace/atta…

pdftotext "/home/daytona/workspace/attachments/3ccaded2-78ff-4579-9180-d585ad8b5…

# Extract pptx style info using python-pptx via pip install pip install python-p…

python3 -c " from pptx import Presentation from pptx.util import Inches, Pt from…

python3 -c " from pptx import Presentation from pptx.util import Inches, Pt impo…

mkdir -p /home/daytona/workspace/apc-presentation && ls /home/daytona/workspace/…

~/apc-presentation/build.js

const pptxgen = require("pptxgenjs");

const pres = new pptxgen();
pres.layout = "LAYOUT_4x3"; // 10" x 7.5" matching reference
pres.title = "Macrophage as Antigen Presenting Cell";

// ─── STYLE CONSTANTS ───────────────────────────────────────────────────────
const BG = "FFFFFF";
const BLACK = "000000";
const DARK_BLUE = "1F3864";
const MED_BLUE = "2E75B6";
const LIGHT_BLUE = "D6E4F0";
const ACCENT = "2E75B6";
const GRAY_LINE = "BFBFBF";

const TITLE_FONT = "Calibri";
const BODY_FONT = "Calibri";

// Title slide bar color
const TITLE_BAR = "1F3864";

// Slide dimensions
const W = 10, H = 7.5;

// ─── HELPER: add title bar + content layout ───────────────────────────────
function addTitleBar(slide, titleText) {
  // Blue rectangle at top
  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: 0, w: W, h: 1.1,
    fill: { color: DARK_BLUE },
    line: { color: DARK_BLUE }
  });
  // Title text
  slide.addText(titleText, {
    x: 0.3, y: 0, w: W - 0.6, h: 1.1,
    fontSize: 26, bold: true, color: "FFFFFF",
    fontFace: TITLE_FONT, valign: "middle", align: "left",
    margin: 0
  });
  // Bottom accent line
  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: H - 0.32, w: W, h: 0.32,
    fill: { color: DARK_BLUE },
    line: { color: DARK_BLUE }
  });
}

// Helper: simple bullet slide
function addBulletSlide(title, bullets, opts = {}) {
  const slide = pres.addSlide();
  slide.background = { color: BG };
  addTitleBar(slide, title);
  const bodyY = opts.bodyY || 1.25;
  const bodyH = opts.bodyH || (H - bodyY - 0.5);
  const fontSize = opts.fontSize || 18;
  const items = bullets.map((b, i) => {
    const last = i === bullets.length - 1;
    if (typeof b === "string") {
      return { text: b, options: { bullet: { code: "2022" }, breakLine: !last, fontSize, color: BLACK, fontFace: BODY_FONT, indentLevel: 0 } };
    }
    // object: {text, bold, indent, color, fontSize}
    return {
      text: b.text,
      options: {
        bullet: b.noBullet ? false : { code: "2022" },
        breakLine: !last,
        fontSize: b.fontSize || fontSize,
        bold: b.bold || false,
        color: b.color || BLACK,
        fontFace: BODY_FONT,
        indentLevel: b.indent || 0
      }
    };
  });
  slide.addText(items, {
    x: 0.4, y: bodyY, w: W - 0.8, h: bodyH,
    valign: "top", margin: [4, 4, 4, 4]
  });
  return slide;
}

// Helper: two-column table slide
function addTableSlide(title, headers, rows, opts = {}) {
  const slide = pres.addSlide();
  slide.background = { color: BG };
  addTitleBar(slide, title);

  const tableY = opts.tableY || 1.3;
  const tableH = opts.tableH || (H - tableY - 0.5);
  const colW = opts.colW || [(W - 0.8) / headers.length];
  const colWArr = Array.isArray(colW) ? colW : headers.map(() => (W - 0.8) / headers.length);

  const headerRow = headers.map(h => ({
    text: h,
    options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, align: "center", fontSize: 15, fontFace: TITLE_FONT }
  }));

  const tableRows = [headerRow, ...rows.map((row, ri) =>
    row.map(cell => ({
      text: cell,
      options: {
        fontSize: 13,
        color: BLACK,
        fill: { color: ri % 2 === 0 ? LIGHT_BLUE : "EAF2FA" },
        align: "left",
        fontFace: BODY_FONT,
        valign: "middle"
      }
    }))
  )];

  slide.addTable(tableRows, {
    x: 0.4, y: tableY, w: W - 0.8,
    rowH: 0.38,
    border: { type: "solid", color: "AABDD4", pt: 0.5 },
    colW: colWArr
  });

  return slide;
}

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 1 – TITLE SLIDE
// ═══════════════════════════════════════════════════════════════════════════
{
  const slide = pres.addSlide();
  slide.background = { color: BG };

  // Top full-width dark blue bar
  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: 0, w: W, h: 1.8,
    fill: { color: DARK_BLUE }, line: { color: DARK_BLUE }
  });
  slide.addText("ANTIGEN PRESENTING CELLS", {
    x: 0.4, y: 0, w: W - 0.8, h: 1.8,
    fontSize: 32, bold: true, color: "FFFFFF",
    fontFace: TITLE_FONT, align: "center", valign: "middle"
  });

  // Subtitle box
  slide.addShape(pres.ShapeType.rect, {
    x: 1.5, y: 2.2, w: 7, h: 0.7,
    fill: { color: LIGHT_BLUE }, line: { color: MED_BLUE, pt: 1.5 }
  });
  slide.addText("Macrophage as a Professional APC", {
    x: 1.5, y: 2.2, w: 7, h: 0.7,
    fontSize: 20, bold: true, color: DARK_BLUE,
    fontFace: TITLE_FONT, align: "center", valign: "middle"
  });

  // Presenter info
  slide.addText([
    { text: "Dermatology Residency Presentation\n", options: { fontSize: 16, color: "555555", fontFace: BODY_FONT } },
    { text: "Department of Dermatology", options: { fontSize: 15, color: "777777", fontFace: BODY_FONT } }
  ], {
    x: 1.5, y: 3.3, w: 7, h: 1.2,
    align: "center", valign: "middle"
  });

  // Bottom bar
  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: H - 0.32, w: W, h: 0.32,
    fill: { color: DARK_BLUE }, line: { color: DARK_BLUE }
  });
}

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 2 – CONTENTS
// ═══════════════════════════════════════════════════════════════════════════
addBulletSlide("Contents", [
  { text: "1. What is an Antigen Presenting Cell?", bold: false, noBullet: false },
  { text: "2. Origin and Distribution of Macrophages", bold: false },
  { text: "3. Key Surface Molecules for APC Function", bold: false },
  { text: "4. MHC Class II Antigen Processing Pathway", bold: false },
  { text: "5. Two-Signal Model for T Cell Activation", bold: false },
  { text: "6. MHC Class I vs Class II Presentation", bold: false },
  { text: "7. Macrophage Activation Feedback Loop", bold: false },
  { text: "8. Macrophages vs Dendritic Cells", bold: false },
  { text: "9. APC Function in Disease States", bold: false },
  { text: "10. M1 vs M2 Polarization", bold: false },
  { text: "11. Summary & References", bold: false }
], { fontSize: 17 });

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 3 – WHAT IS AN APC?
// ═══════════════════════════════════════════════════════════════════════════
{
  const slide = pres.addSlide();
  slide.background = { color: BG };
  addTitleBar(slide, "What is an Antigen Presenting Cell (APC)?");

  // Definition box
  slide.addShape(pres.ShapeType.rect, {
    x: 0.4, y: 1.3, w: W - 0.8, h: 1.1,
    fill: { color: LIGHT_BLUE }, line: { color: MED_BLUE, pt: 1 }
  });
  slide.addText("A cell that captures, processes, and displays antigenic peptides on its surface in complex with MHC molecules, allowing T lymphocytes to recognize and respond to them.", {
    x: 0.5, y: 1.3, w: W - 1.0, h: 1.1,
    fontSize: 15, color: DARK_BLUE, fontFace: BODY_FONT,
    italic: true, valign: "middle", align: "left"
  });

  // Three professional APCs
  slide.addText("The Three Professional APCs", {
    x: 0.4, y: 2.55, w: W - 0.8, h: 0.4,
    fontSize: 18, bold: true, color: DARK_BLUE, fontFace: TITLE_FONT
  });

  const apcs = [
    { label: "Macrophages", sub: "Phagocytosis +\nAntigen presentation" },
    { label: "Dendritic Cells", sub: "Most efficient\nfor naive T cells" },
    { label: "B Lymphocytes", sub: "BCR-mediated\nantigen uptake" }
  ];
  const boxW = 2.6, boxH = 1.4, startX = 0.65, boxY = 3.1, gap = 0.45;
  apcs.forEach((apc, i) => {
    const x = startX + i * (boxW + gap);
    slide.addShape(pres.ShapeType.rect, {
      x, y: boxY, w: boxW, h: boxH,
      fill: { color: i === 0 ? DARK_BLUE : MED_BLUE },
      line: { color: DARK_BLUE }
    });
    slide.addText([
      { text: apc.label + "\n", options: { bold: true, fontSize: 16, color: "FFFFFF", fontFace: TITLE_FONT } },
      { text: apc.sub, options: { fontSize: 13, color: "E8F0FB", fontFace: BODY_FONT } }
    ], {
      x, y: boxY, w: boxW, h: boxH,
      align: "center", valign: "middle"
    });
  });

  slide.addText("Macrophages are unique: simultaneously phagocytes, innate effectors, and professional APCs", {
    x: 0.4, y: 4.7, w: W - 0.8, h: 0.5,
    fontSize: 14, color: "555555", italic: true, fontFace: BODY_FONT, align: "center"
  });

  // Bottom bar
  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: H - 0.32, w: W, h: 0.32,
    fill: { color: DARK_BLUE }, line: { color: DARK_BLUE }
  });
}

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 4 – ORIGIN AND DISTRIBUTION
// ═══════════════════════════════════════════════════════════════════════════
{
  const slide = pres.addSlide();
  slide.background = { color: BG };
  addTitleBar(slide, "Origin and Distribution of Macrophages");

  slide.addText([
    { text: "Bone Marrow Progenitors", options: { bold: true, fontSize: 15, color: DARK_BLUE, fontFace: TITLE_FONT, breakLine: true } },
    { text: "  ↓   Monocytes circulate ~3 days in blood", options: { fontSize: 14, color: BLACK, fontFace: BODY_FONT, breakLine: true } },
    { text: "  ↓   Migrate into tissues → differentiate into tissue-resident macrophages", options: { fontSize: 14, color: BLACK, fontFace: BODY_FONT } }
  ], {
    x: 0.4, y: 1.25, w: W - 0.8, h: 0.95,
    valign: "top"
  });

  // Table: tissue macrophages
  const headerRow = [
    { text: "Tissue / Location", options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, fontSize: 14, fontFace: TITLE_FONT, align: "center" } },
    { text: "Macrophage Name", options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, fontSize: 14, fontFace: TITLE_FONT, align: "center" } }
  ];
  const tRows = [
    ["Liver", "Kupffer cells"],
    ["Lung", "Alveolar macrophages"],
    ["Brain", "Microglia"],
    ["Bone", "Osteoclasts"],
    ["Connective tissue", "Histiocytes"],
    ["Spleen / Lymph nodes", "Free macrophages"],
    ["Kidney (mesangium)", "Mesangial cells"],
    ["Skin", "Dermal macrophages"]
  ];
  const tableRows = [
    headerRow,
    ...tRows.map((r, i) => r.map(cell => ({
      text: cell,
      options: { fontSize: 13, color: BLACK, fill: { color: i % 2 === 0 ? LIGHT_BLUE : "EAF2FA" }, fontFace: BODY_FONT, valign: "middle" }
    })))
  ];
  slide.addTable(tableRows, {
    x: 0.4, y: 2.35, w: W - 0.8,
    rowH: 0.38,
    colW: [4.6, 4.6],
    border: { type: "solid", color: "AABDD4", pt: 0.5 }
  });

  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: H - 0.32, w: W, h: 0.32,
    fill: { color: DARK_BLUE }, line: { color: DARK_BLUE }
  });
}

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 5 – KEY SURFACE MOLECULES
// ═══════════════════════════════════════════════════════════════════════════
{
  const slide = pres.addSlide();
  slide.background = { color: BG };
  addTitleBar(slide, "Key Surface Molecules for APC Function");

  const headerRow = [
    { text: "Molecule", options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, fontSize: 13, fontFace: TITLE_FONT, align: "center" } },
    { text: "Role", options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, fontSize: 13, fontFace: TITLE_FONT, align: "center" } }
  ];
  const rows = [
    ["MHC class II (HLA-DR, DP, DQ)", "Presents processed peptide to CD4+ T cells"],
    ["MHC class I", "Presents endogenous/viral peptides to CD8+ T cells"],
    ["CD80 / CD86 (B7 family)", "Costimulatory signals to T cells"],
    ["CD40", "Receives activating signal from CD40L on T cells"],
    ["TLRs, NLRs (PRRs)", "Detect PAMPs to trigger phagocytosis"],
    ["Fc receptors (FcγR)", "Opsonized antigen uptake"],
    ["Complement receptors (CR1, CR3)", "Enhance phagocytosis"],
    ["Invariant chain (CD74)", "Protects MHC II peptide groove during biosynthesis"]
  ];
  const tableRows = [
    headerRow,
    ...rows.map((r, i) => r.map(cell => ({
      text: cell,
      options: { fontSize: 12.5, color: BLACK, fill: { color: i % 2 === 0 ? LIGHT_BLUE : "EAF2FA" }, fontFace: BODY_FONT, valign: "middle" }
    })))
  ];
  slide.addTable(tableRows, {
    x: 0.4, y: 1.25, w: W - 0.8,
    rowH: 0.52,
    colW: [3.8, 5.4],
    border: { type: "solid", color: "AABDD4", pt: 0.5 }
  });

  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: H - 0.32, w: W, h: 0.32,
    fill: { color: DARK_BLUE }, line: { color: DARK_BLUE }
  });
}

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 6 – MHC CLASS II PATHWAY OVERVIEW
// ═══════════════════════════════════════════════════════════════════════════
addBulletSlide("MHC Class II Antigen Processing Pathway", [
  { text: "Step 1: Antigen Uptake", bold: true, noBullet: false, fontSize: 17, color: DARK_BLUE },
  { text: "Phagocytosis (large particles, opsonized bacteria)", indent: 1, fontSize: 15 },
  { text: "Macropinocytosis (bulk fluid uptake)", indent: 1, fontSize: 15 },
  { text: "Receptor-mediated endocytosis (Fc, complement, mannose receptors)", indent: 1, fontSize: 15 },
  { text: "Step 2: Phagosome Formation", bold: true, noBullet: false, fontSize: 17, color: DARK_BLUE },
  { text: "Ingested material enclosed in phagosome (neutral pH)", indent: 1, fontSize: 15 },
  { text: "Step 3: Acidification and Lysosomal Fusion", bold: true, noBullet: false, fontSize: 17, color: DARK_BLUE },
  { text: "Phagosome + lysosome → phagolysosome; V-ATPase drops pH to ~4.5-5", indent: 1, fontSize: 15 },
  { text: "Cathepsins & GILT (disulfide bond breaker) degrade antigen into peptides of 13-25 aa", indent: 1, fontSize: 15 }
], { bodyY: 1.25, bodyH: 5.9, fontSize: 16 });

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 7 – MHC CLASS II PATHWAY (STEPS 4–6)
// ═══════════════════════════════════════════════════════════════════════════
addBulletSlide("MHC Class II Pathway (continued)", [
  { text: "Step 4: MHC Class II Biosynthesis and Transport", bold: true, noBullet: false, fontSize: 17, color: DARK_BLUE },
  { text: "MHC II (α + β chains) synthesized in ER", indent: 1, fontSize: 15 },
  { text: "Invariant chain (Ii, CD74) binds peptide groove (CLIP segment) → prevents premature loading", indent: 1, fontSize: 15 },
  { text: "MHC II-Ii complex travels: ER → Golgi → late endosome", indent: 1, fontSize: 15 },
  { text: "Step 5: CLIP Removal and Peptide Loading", bold: true, noBullet: false, fontSize: 17, color: DARK_BLUE },
  { text: "Cathepsin S cleaves invariant chain → leaves only CLIP in groove", indent: 1, fontSize: 15 },
  { text: "HLA-DM (accessory molecule) catalyzes exchange of CLIP for high-affinity antigenic peptide", indent: 1, fontSize: 15 },
  { text: "Only stable peptide-MHC II complexes are retained", indent: 1, fontSize: 15 },
  { text: "Step 6: Surface Display", bold: true, noBullet: false, fontSize: 17, color: DARK_BLUE },
  { text: "Peptide:MHC II complex transported to cell surface", indent: 1, fontSize: 15 },
  { text: "Recognized by TCR of CD4+ helper T cells", indent: 1, fontSize: 15 }
], { bodyY: 1.25, bodyH: 5.9, fontSize: 16 });

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 8 – PATHWAY DIAGRAM (TEXT-BASED FLOWCHART)
// ═══════════════════════════════════════════════════════════════════════════
{
  const slide = pres.addSlide();
  slide.background = { color: BG };
  addTitleBar(slide, "MHC Class II Pathway – Summary Diagram");

  const steps = [
    { text: "Extracellular Antigen (bacteria / foreign protein)", color: DARK_BLUE },
    { text: "↓  Phagocytosis / Endocytosis", color: BLACK },
    { text: "Phagosome  (neutral pH)", color: MED_BLUE },
    { text: "↓  Lysosome fusion + V-ATPase (pH ~4.5)", color: BLACK },
    { text: "Phagolysosome — Cathepsins + GILT active", color: MED_BLUE },
    { text: "↓  Antigen degraded → Peptide fragments (13-25 aa)", color: BLACK },
    { text: "Late endosome + MHC II-Ii complex", color: MED_BLUE },
    { text: "↓  HLA-DM removes CLIP; high-affinity peptide loads", color: BLACK },
    { text: "Peptide : MHC II complex → Cell Surface", color: DARK_BLUE },
    { text: "↓  Recognized by CD4+ T cell TCR", color: BLACK }
  ];

  const boxH = 0.44, startY = 1.25, gap = 0.02;
  steps.forEach((s, i) => {
    const isBullet = s.text.startsWith("↓");
    slide.addText(s.text, {
      x: isBullet ? 0.8 : 0.4,
      y: startY + i * (boxH + gap),
      w: W - 0.8,
      h: boxH,
      fontSize: 15,
      bold: !isBullet,
      color: s.color,
      fontFace: BODY_FONT,
      fill: isBullet ? { type: "none" } : { color: i % 4 === 0 ? LIGHT_BLUE : (i % 4 === 2 ? "D6E4F0" : "EAF2FA") },
      align: isBullet ? "left" : "center",
      valign: "middle",
      margin: isBullet ? 0 : [0, 8, 0, 8]
    });
  });

  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: H - 0.32, w: W, h: 0.32,
    fill: { color: DARK_BLUE }, line: { color: DARK_BLUE }
  });
}

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 9 – TWO-SIGNAL MODEL
// ═══════════════════════════════════════════════════════════════════════════
{
  const slide = pres.addSlide();
  slide.background = { color: BG };
  addTitleBar(slide, "Two-Signal Model for T Cell Activation");

  const signals = [
    {
      label: "Signal 1: Antigen-Specific (TCR Signal)",
      bullets: [
        "TCR on CD4+ T cell binds peptide : MHC II complex on macrophage",
        "Alone → causes T cell ANERGY (unresponsiveness), NOT activation"
      ],
      color: DARK_BLUE
    },
    {
      label: "Signal 2: Costimulatory",
      bullets: [
        "CD80/CD86 (B7) on macrophage binds CD28 on T cell",
        "Provides the second signal needed for full T cell activation, proliferation, and cytokine production"
      ],
      color: MED_BLUE
    },
    {
      label: "Signal 3: Cytokines (Polarization)",
      bullets: [
        "IL-12 → drives Th1 differentiation",
        "IL-1, IL-6, TNF-α → amplify inflammation",
        "These polarize the T cell response to the type of pathogen"
      ],
      color: "4A90D9"
    }
  ];

  let curY = 1.3;
  signals.forEach(sig => {
    slide.addShape(pres.ShapeType.rect, {
      x: 0.4, y: curY, w: W - 0.8, h: 0.38,
      fill: { color: sig.color }, line: { color: sig.color }
    });
    slide.addText(sig.label, {
      x: 0.5, y: curY, w: W - 1, h: 0.38,
      fontSize: 16, bold: true, color: "FFFFFF", fontFace: TITLE_FONT, valign: "middle"
    });
    curY += 0.38;
    sig.bullets.forEach(b => {
      slide.addText([{ text: b, options: { bullet: { code: "2022" }, fontSize: 14, color: BLACK, fontFace: BODY_FONT } }], {
        x: 0.6, y: curY, w: W - 1, h: 0.38,
        valign: "middle"
      });
      curY += 0.38;
    });
    curY += 0.1;
  });

  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: H - 0.32, w: W, h: 0.32,
    fill: { color: DARK_BLUE }, line: { color: DARK_BLUE }
  });
}

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 10 – MHC CLASS I vs CLASS II
// ═══════════════════════════════════════════════════════════════════════════
{
  const slide = pres.addSlide();
  slide.background = { color: BG };
  addTitleBar(slide, "MHC Class I vs Class II Presentation");

  const headerRow = [
    { text: "Feature", options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, fontSize: 13, fontFace: TITLE_FONT, align: "center" } },
    { text: "MHC Class II", options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, fontSize: 13, fontFace: TITLE_FONT, align: "center" } },
    { text: "MHC Class I", options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, fontSize: 13, fontFace: TITLE_FONT, align: "center" } }
  ];
  const rows = [
    ["Antigen source", "Extracellular (exogenous)", "Intracellular (endogenous)"],
    ["T cell target", "CD4+ helper T cells", "CD8+ cytotoxic T cells"],
    ["Peptide length", "13-25 amino acids", "8-10 amino acids"],
    ["Processing site", "Phagolysosome / late endosome", "Proteasome → TAP → ER"],
    ["Key molecules", "Invariant chain, HLA-DM", "TAP1/TAP2, tapasin"],
    ["Macrophage role", "Professional APC", "Any infected cell"],
    ["Cross-presentation", "N/A", "Exogenous → MHC I (limited)"]
  ];
  const tableRows = [
    headerRow,
    ...rows.map((r, i) => r.map((cell, ci) => ({
      text: cell,
      options: { fontSize: 13, color: BLACK, fill: { color: i % 2 === 0 ? LIGHT_BLUE : "EAF2FA" }, fontFace: BODY_FONT, valign: "middle", bold: ci === 0 }
    })))
  ];
  slide.addTable(tableRows, {
    x: 0.4, y: 1.25, w: W - 0.8,
    rowH: 0.5,
    colW: [2.7, 3.3, 3.2],
    border: { type: "solid", color: "AABDD4", pt: 0.5 }
  });

  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: H - 0.32, w: W, h: 0.32,
    fill: { color: DARK_BLUE }, line: { color: DARK_BLUE }
  });
}

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 11 – FEEDBACK LOOP
// ═══════════════════════════════════════════════════════════════════════════
addBulletSlide("Macrophage Activation Feedback Loop (Th1)", [
  { text: "Bidirectional communication is the heart of cell-mediated immunity:", bold: true, noBullet: false, fontSize: 16, color: DARK_BLUE },
  { text: "CD4+ Th1 cells recognize peptide : MHC II on macrophage", indent: 1, fontSize: 15 },
  { text: "T cell secretes IFN-γ — the most potent macrophage-activating cytokine", indent: 1, fontSize: 15 },
  { text: "T cell expresses CD40L which binds CD40 on macrophage", indent: 1, fontSize: 15 },
  { text: "Classical Activation (M1) Triggers:", bold: true, noBullet: false, fontSize: 16, color: DARK_BLUE },
  { text: "↑ MHC II and B7 (enhanced APC function)", indent: 1, fontSize: 15 },
  { text: "iNOS induction → nitric oxide (NO) production", indent: 1, fontSize: 15 },
  { text: "↑ Reactive oxygen species (ROS) via NADPH oxidase", indent: 1, fontSize: 15 },
  { text: "Enhanced phagocytosis and intracellular killing", indent: 1, fontSize: 15 },
  { text: "Cytokines: TNF-α, IL-1, IL-12, IL-6, IL-18, IL-23", indent: 1, fontSize: 15 },
  { text: "Clinical relevance: Controls M. tuberculosis, Leishmania through IFN-γ amplification of killing", bold: false, noBullet: false, fontSize: 14, color: "555555" }
], { bodyY: 1.25, bodyH: 5.9 });

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 12 – MACROPHAGES vs DENDRITIC CELLS
// ═══════════════════════════════════════════════════════════════════════════
{
  const slide = pres.addSlide();
  slide.background = { color: BG };
  addTitleBar(slide, "Macrophages vs Dendritic Cells as APCs");

  const headerRow = [
    { text: "Feature", options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, fontSize: 13, fontFace: TITLE_FONT, align: "center" } },
    { text: "Macrophage", options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, fontSize: 13, fontFace: TITLE_FONT, align: "center" } },
    { text: "Dendritic Cell", options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, fontSize: 13, fontFace: TITLE_FONT, align: "center" } }
  ];
  const rows = [
    ["Primary role", "Phagocytosis + Killing", "Antigen presentation"],
    ["Tissue resident", "Yes", "Yes (immature)"],
    ["Migration to lymph node", "Limited", "Yes (mature DC)"],
    ["Naive T cell priming", "Weak", "Strong (most efficient)"],
    ["Costimulatory molecules", "Induced by activation", "Constitutively high"],
    ["MHC II expression", "Induced, lower level", "Very high after maturation"],
    ["Cross-presentation", "Limited", "Major role"],
    ["Best at", "Effector/memory T cell restimulation", "Primary T cell priming"]
  ];
  const tableRows = [
    headerRow,
    ...rows.map((r, i) => r.map((cell, ci) => ({
      text: cell,
      options: { fontSize: 12.5, color: BLACK, fill: { color: i % 2 === 0 ? LIGHT_BLUE : "EAF2FA" }, fontFace: BODY_FONT, valign: "middle", bold: ci === 0 }
    })))
  ];
  slide.addTable(tableRows, {
    x: 0.4, y: 1.25, w: W - 0.8,
    rowH: 0.48,
    colW: [2.7, 3.3, 3.2],
    border: { type: "solid", color: "AABDD4", pt: 0.5 }
  });

  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: H - 0.32, w: W, h: 0.32,
    fill: { color: DARK_BLUE }, line: { color: DARK_BLUE }
  });
}

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 13 – APC FUNCTION IN DISEASE STATES
// ═══════════════════════════════════════════════════════════════════════════
{
  const slide = pres.addSlide();
  slide.background = { color: BG };
  addTitleBar(slide, "Macrophage APC Function in Disease States");

  const diseases = [
    {
      name: "Tuberculosis (M. tuberculosis)",
      points: [
        "Mycobacteria inhibit phagolysosome fusion and acidification",
        "Peptides still reach MHC II → presented to Th1 cells",
        "Th1 → IFN-γ → granuloma formation (containment mechanism)"
      ]
    },
    {
      name: "HIV Infection",
      points: [
        "HIV infects macrophages via CD4 + CCR5",
        "Impairs MHC II surface expression → reduced APC function",
        "Loss of APC capacity contributes to immune evasion"
      ]
    },
    {
      name: "Autoimmunity (RA, SLE)",
      points: [
        "Macrophages present self-antigens on MHC II → autoreactive T cells",
        "Excess IL-1, TNF-α drives tissue damage",
        "Targets of anti-TNF, IL-1 blockers, hydroxychloroquine (impairs lysosomal acidification)"
      ]
    },
    {
      name: "Tumor Microenvironment",
      points: [
        "TAMs polarized to M2 (alternative) phenotype",
        "M2 macrophages: reduced APC function, suppress T cell responses",
        "Key mechanism of tumor immune escape"
      ]
    }
  ];

  let curY = 1.25;
  diseases.forEach((d, di) => {
    slide.addShape(pres.ShapeType.rect, {
      x: 0.4, y: curY, w: W - 0.8, h: 0.32,
      fill: { color: di % 2 === 0 ? DARK_BLUE : MED_BLUE }, line: { color: DARK_BLUE }
    });
    slide.addText(d.name, {
      x: 0.5, y: curY, w: W - 1, h: 0.32,
      fontSize: 13.5, bold: true, color: "FFFFFF", fontFace: TITLE_FONT, valign: "middle"
    });
    curY += 0.32;
    d.points.forEach(p => {
      slide.addText([{ text: p, options: { bullet: { code: "2022" }, fontSize: 12, color: BLACK, fontFace: BODY_FONT } }], {
        x: 0.6, y: curY, w: W - 1, h: 0.33,
        valign: "middle"
      });
      curY += 0.33;
    });
    curY += 0.06;
  });

  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: H - 0.32, w: W, h: 0.32,
    fill: { color: DARK_BLUE }, line: { color: DARK_BLUE }
  });
}

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 14 – M1 vs M2 POLARIZATION
// ═══════════════════════════════════════════════════════════════════════════
{
  const slide = pres.addSlide();
  slide.background = { color: BG };
  addTitleBar(slide, "M1 vs M2 Macrophage Polarization and APC Function");

  const headerRow = [
    { text: "Property", options: { bold: true, color: "FFFFFF", fill: { color: DARK_BLUE }, fontSize: 13, fontFace: TITLE_FONT, align: "center" } },
    { text: "M1 (Classical)", options: { bold: true, color: "FFFFFF", fill: { color: "C0392B" }, fontSize: 13, fontFace: TITLE_FONT, align: "center" } },
    { text: "M2 (Alternative)", options: { bold: true, color: "FFFFFF", fill: { color: "27AE60" }, fontSize: 13, fontFace: TITLE_FONT, align: "center" } }
  ];
  const rows = [
    ["Trigger", "IFN-γ, LPS", "IL-4, IL-13, IL-10"],
    ["MHC II expression", "High", "Low"],
    ["Costimulatory molecules", "High (B7)", "Low"],
    ["APC function", "Strong", "Weak"],
    ["Cytokines", "IL-12, IL-23, TNF, IL-1", "IL-10, TGF-β, IL-4"],
    ["T cell outcome", "Th1 / Th17 response", "Th2 / Treg response"],
    ["Role", "Killing, inflammation", "Repair, tolerance, tumor promotion"]
  ];
  const tableRows = [
    headerRow,
    ...rows.map((r, i) => [
      { text: r[0], options: { fontSize: 13, color: BLACK, fill: { color: i % 2 === 0 ? LIGHT_BLUE : "EAF2FA" }, fontFace: BODY_FONT, bold: true, valign: "middle" } },
      { text: r[1], options: { fontSize: 13, color: BLACK, fill: { color: i % 2 === 0 ? "FDECEA" : "FDEDED" }, fontFace: BODY_FONT, valign: "middle" } },
      { text: r[2], options: { fontSize: 13, color: BLACK, fill: { color: i % 2 === 0 ? "E8F8EF" : "D5F5E3" }, fontFace: BODY_FONT, valign: "middle" } }
    ])
  ];
  slide.addTable(tableRows, {
    x: 0.4, y: 1.25, w: W - 0.8,
    rowH: 0.5,
    colW: [2.8, 3.2, 3.2],
    border: { type: "solid", color: "AABDD4", pt: 0.5 }
  });

  slide.addShape(pres.ShapeType.rect, {
    x: 0, y: H - 0.32, w: W, h: 0.32,
    fill: { color: DARK_BLUE }, line: { color: DARK_BLUE }
  });
}

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 15 – SUMMARY
// ═══════════════════════════════════════════════════════════════════════════
addBulletSlide("Summary: Key Points", [
  "Macrophages are professional APCs bridging innate and adaptive immunity",
  "They capture antigen by phagocytosis and process it via the phagolysosomal pathway",
  "Antigenic peptides (13-25 aa) loaded onto MHC II via the invariant chain / CLIP / HLA-DM system",
  "Peptide : MHC II complex displayed on surface for CD4+ T cell recognition",
  "T cell activation requires TWO signals: TCR-MHC II (Signal 1) + CD28-B7 costimulation (Signal 2)",
  "Macrophage IL-12, TNF, IL-1 provide Signal 3 (cytokine polarization)",
  "Activated Th1 cells feed back via IFN-γ and CD40L → M1 macrophage amplification",
  "Macrophage APC function impaired in M. tuberculosis, HIV, tumor microenvironments",
  "Dendritic cells: primary APCs for naive T cell priming; Macrophages: critical for effector/memory T cell restimulation"
], { bodyY: 1.25, bodyH: 5.9, fontSize: 16 });

// ═══════════════════════════════════════════════════════════════════════════
// SLIDE 16 – REFERENCES
// ═══════════════════════════════════════════════════════════════════════════
addBulletSlide("References", [
  { text: "Mescher M.F. – Histology: A Text and Atlas – Monocyte-macrophage as APC, MHC II presentation", fontSize: 15, bold: false },
  { text: "Murphy K., Weaver C. – Janeway's Immunobiology, 10th Edition – MHC class II antigen processing, invariant chain, HLA-DM, Th1-macrophage interaction", fontSize: 15, bold: false },
  { text: "Roitt I. – Roitt's Essential Immunology – Cell-mediated immunity, professional APCs", fontSize: 15, bold: false },
  { text: "Rheumatology, 2-Volume Set (Elsevier 2022) – Macrophage cytokine production and APC function", fontSize: 15, bold: false },
  { text: "Murray R., et al. – Medical Microbiology, 9th Edition – Macrophage as APC in bacterial/viral infections", fontSize: 15, bold: false },
  { text: "Abbas A.K., Lichtman A.H., Pillai S. – Cellular and Molecular Immunology, 10th Edition", fontSize: 15, bold: false }
], { bodyY: 1.25, bodyH: 5.9, fontSize: 15 });

// ═══════════════════════════════════════════════════════════════════════════
// WRITE FILE
// ═══════════════════════════════════════════════════════════════════════════
pres.writeFile({ fileName: "/home/daytona/workspace/apc-presentation/Antigen_Presenting_Cell.pptx" })
  .then(() => console.log("Done: /home/daytona/workspace/apc-presentation/Antigen_Presenting_Cell.pptx"))
  .catch(err => { console.error(err); process.exit(1); });

cd /home/daytona/workspace/apc-presentation && node build.js 2>&1

ls -lh /home/daytona/workspace/apc-presentation/Antigen_Presenting_Cell.pptx

ls -lh /home/daytona/workspace/apc-presentation/ && file /home/daytona/workspace…

cd /home/daytona/workspace/apc-presentation && node build.js 2>&1 && ls -lh Anti…

ls -lh /home/daytona/workspace/apc-presentation/ && cp /home/daytona/workspace/a…

cd /home/daytona/workspace && zip APC_Presentation.zip APC_Presentation.pptx && …

# Regenerate fresh with node directly into workspace root cd /home/daytona/works…

cd /home/daytona/workspace/apc-presentation && node build.js 2>&1 # now copy usi…

# Write directly to workspace root using node cd /home/daytona/workspace/apc-pre…

# Write fresh pptx directly to workspace root (not a subdirectory) cd /home/dayt…

find /home/daytona -name "pptxgenjs" -type d 2>/dev/null | head -5 find /usr -na…