What is the specific focus of your buffy coat thesis? · What degree/level is this thesis for? · Where will you collect data?

febrile neutropenia hematological malignancy management outcomes

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febrile neutropenia leukemia Nepal South Asia microbiology bacteremia

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PMID: 38023414

granulocyte transfusion neutropenia infection outcomes mortality

https://pmc.ncbi.nlm.nih.gov/articles/PMC10658032

ASH Blood journal submission guidelines hematology clinical trial original article 2024

ls -la /home/daytona/workspace/ 2>/dev/null || mkdir -p /home/daytona/workspace/fn-thesis && echo "workspace ready"

mkdir -p /home/daytona/workspace/fn-thesis && python3 << 'PYEOF' import openpyxl from openpyxl.styles import ( PatternFill, Font, Alignment, Border, Side, GradientFill ) from openpyxl.utils import get_column_letter from openpyxl.worksheet.datavalidation import DataValidation from openpyxl.styles.numbers import FORMAT_DATE_DDMMYY import openpyxl.styles.colors as colors wb = openpyxl.Workbook() # ─── Color palette ─────────────────────────────────────────────── COL_HEADER_DARK = "1F3864" # dark navy - sheet tab / main header COL_HEADER_MID = "2E75B6" # mid blue - section headers COL_HEADER_LIGHT = "BDD7EE" # pale blue - sub-headers COL_GT_ARM = "E2EFDA" # pale green - GT-arm rows COL_ST_ARM = "FFF2CC" # pale yellow- ST-arm rows COL_OUTCOME = "FCE4D6" # pale orange- outcome cells COL_REQUIRED = "FFD7D7" # pale red - mandatory fields COL_CALC = "F2F2F2" # grey - auto-calculated COL_WHITE = "FFFFFF" COL_YELLOW_HL = "FFFF00" def hdr(ws, row, col, text, bg=COL_HEADER_MID, fg="FFFFFF", bold=True, sz=11, wrap=True, merge_to=None): cell = ws.cell(row=row, column=col, value=text) cell.fill = PatternFill("solid", fgColor=bg) cell.font = Font(bold=bold, color=fg, size=sz, name="Arial") cell.alignment = Alignment(horizontal="center", vertical="center", wrap_text=wrap) if merge_to: ws.merge_cells(start_row=row, start_column=col, end_row=row, end_column=merge_to) return cell def lbl(ws, row, col, text, bg=COL_HEADER_LIGHT, bold=False, sz=9, wrap=True): cell = ws.cell(row=row, column=col, value=text) cell.fill = PatternFill("solid", fgColor=bg) cell.font = Font(bold=bold, color="1F3864", size=sz, name="Arial") cell.alignment = Alignment(horizontal="left", vertical="center", wrap_text=wrap) return cell def inp(ws, row, col, value="", bg=COL_WHITE, sz=9): cell = ws.cell(row=row, column=col, value=value) cell.fill = PatternFill("solid", fgColor=bg) cell.font = Font(size=sz, name="Arial") cell.alignment = Alignment(horizontal="left", vertical="center", wrap_text=True) return cell def thin_border(ws, min_row, min_col, max_row, max_col): thin = Side(style="thin", color="AAAAAA") for row in ws.iter_rows(min_row=min_row, min_col=min_col, max_row=max_row, max_col=max_col): for cell in row: cell.border = Border(top=thin, left=thin, right=thin, bottom=thin) def add_dv_list(ws, formula1, sq_ref): dv = DataValidation(type="list", formula1=formula1, allow_blank=True, showDropDown=False) dv.showErrorMessage = True dv.error = "Please select from list" dv.errorTitle = "Invalid entry" ws.add_data_validation(dv) dv.sqref = sq_ref return dv # ═══════════════════════════════════════════════════════════════════ # SHEET 1 - COVER / INSTRUCTIONS # ═══════════════════════════════════════════════════════════════════ ws0 = wb.active ws0.title = "📋 Instructions" ws0.sheet_properties.tabColor = COL_HEADER_DARK ws0.column_dimensions["A"].width = 5 ws0.column_dimensions["B"].width = 60 ws0.column_dimensions["C"].width = 40 hdr(ws0, 1, 1, "FEBRILE NEUTROPENIA IN HEMATOLOGICAL MALIGNANCIES — RESEARCH DATA ENTRY SYSTEM", bg=COL_HEADER_DARK, fg="FFFFFF", bold=True, sz=14, merge_to=3) ws0.row_dimensions[1].height = 35 rows_info = [ (3, "Civil Service Hospital, Kathmandu, Nepal", "DM Thesis — Clinical Hematology"), (4, "Study: Buffy Coat-Derived Granulocyte Transfusion vs Standard Care in High-Risk FN", ""), (5, "Investigator: ___________________________ Supervisor: ___________________________", ""), (6, "Ethical Approval No.: _________________ CTRI Reg No.: ________________________", ""), ] for r, t1, t2 in rows_info: ws0.cell(row=r, column=2, value=t1).font = Font(bold=True, size=10, name="Arial", color="1F3864") ws0.cell(row=r, column=3, value=t2).font = Font(size=9, name="Arial", color="2E75B6") hdr(ws0, 8, 1, "SHEET GUIDE", bg=COL_HEADER_MID, merge_to=3, sz=11) sheets_guide = [ ("1. 👤 Patient_Demographics", "Age, sex, address, BMI, comorbidities, ECOG — fill once per patient"), ("2. 🩸 Malignancy_Chemo", "Diagnosis, cytogenetics, chemotherapy regimen, disease status"), ("3. 🌡️ FN_Episode", "FN definition, MASCC score, clinical site, sepsis criteria"), ("4. 🔬 Lab_Microbiology", "CBC daily, biochemistry, cultures, inflammatory markers, imaging"), ("5. 💉 GT_Transfusion_Log", "Buffy coat prep details, dose, adverse events — GT arm only"), ("6. 💊 Treatment", "Antibiotics, antifungals, G-CSF, supportive care, ICU"), ("7. ✅ Outcomes", "Primary/secondary outcomes, mortality, ANC recovery, cost"), ("8. 📅 Follow_Up", "Day 30/60/90 follow-up, survival, disease status"), ("9. 📊 Summary_Dashboard", "Auto-calculated summary statistics for quick review"), ("10. 📝 Codebook", "Variable definitions, normal ranges, coding guide"), ] for i, (sheet, desc) in enumerate(sheets_guide): r = 9 + i ws0.cell(row=r, column=2, value=sheet).font = Font(bold=True, size=10, name="Arial", color="1F3864") ws0.cell(row=r, column=2).fill = PatternFill("solid", fgColor=COL_HEADER_LIGHT) ws0.cell(row=r, column=3, value=desc).font = Font(size=9, name="Arial") ws0.row_dimensions[r].height = 16 hdr(ws0, 20, 1, "DATA ENTRY RULES", bg=COL_HEADER_DARK, merge_to=3, sz=11) rules = [ "🔴 RED cells = MANDATORY — must not be left blank", "🟡 YELLOW cells = Auto-calculated — do not type in these cells", "🟢 GREEN cells = GT arm only — leave blank for ST arm patients", "📌 Use dropdown menus wherever provided — do NOT type free text in dropdown cells", "📅 Enter all dates as DD/MM/YYYY format", "🔢 Enter lab values as numbers only — units are in the column header", "❌ For negative/absent findings, select 'No' or enter '0' — do NOT leave blank", "💾 Save after each patient entry — use Study_ID as filename suffix", "🔒 Do not modify column headers or add/delete rows in data sheets", ] for i, rule in enumerate(rules): r = 21 + i ws0.cell(row=r, column=2, value=rule).font = Font(size=9, name="Arial", color="1F3864") ws0.row_dimensions[r].height = 14 thin_border(ws0, 1, 1, 30, 3) # ═══════════════════════════════════════════════════════════════════ # SHEET 2 - PATIENT DEMOGRAPHICS # ═══════════════════════════════════════════════════════════════════ ws1 = wb.create_sheet("👤 Patient_Demographics") ws1.sheet_properties.tabColor = "2E75B6" # Column widths col_widths = [5, 18, 22, 25, 12, 14, 14, 14, 14, 14, 14, 14, 22, 22, 22, 22] for i, w in enumerate(col_widths, 1): ws1.column_dimensions[get_column_letter(i)].width = w hdr(ws1, 1, 1, "PATIENT DEMOGRAPHICS & BASELINE DATA", bg=COL_HEADER_DARK, fg="FFFFFF", bold=True, sz=13, merge_to=16) ws1.row_dimensions[1].height = 30 # Sub-headers row headers = [ "#", "Study ID\n(Mandatory)", "Enrollment\nDate (DD/MM/YY)", "Arm\n(GT / ST)", "Age\n(Years)", "Sex\n(M/F/O)", "Height\n(cm)", "Weight\n(kg)", "BMI\n(Auto)", "ECOG\n(0-4)", "District", "Urban/Rural", "Monthly Income\n(NPR)", "Insurance\n(Yes/No)", "Comorbidities\n(see codebook)", "Referral Source" ] for col, h in enumerate(headers, 1): c = lbl(ws1, 2, col, h, bg=COL_HEADER_MID, bold=True) c.font = Font(bold=True, color="FFFFFF", size=9, name="Arial") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws1.row_dimensions[2].height = 32 # Extra info row extra = [ "", "Format: CSH-001", "First FN episode date", "Randomized arm", "Numeric", "M/F/Other", "Numeric", "Numeric", "=Wt/(Ht/100)²", "0=Normal, 4=Bedridden", "Free text", "Urban/Peri-urban/Rural", "Approximate", "Yes/No/Type", "DM,HTN,CKD,CLD,IHD,HIV,TB,None", "OPD/IPD/Referral" ] for col, e in enumerate(extra, 1): c = ws1.cell(row=3, column=col, value=e) c.fill = PatternFill("solid", fgColor="E8F4FD") c.font = Font(italic=True, size=8, name="Arial", color="555555") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws1.row_dimensions[3].height = 20 # Data rows (20 patients) for row in range(4, 24): ws1.cell(row=row, column=1, value=row-3) # Study ID - mandatory red c = ws1.cell(row=row, column=2, value="") c.fill = PatternFill("solid", fgColor=COL_REQUIRED) # Enrollment date ws1.cell(row=row, column=3, value="") # Arm dropdown c_arm = ws1.cell(row=row, column=4, value="") c_arm.fill = PatternFill("solid", fgColor=COL_REQUIRED) # Age ws1.cell(row=row, column=5, value="") # Sex ws1.cell(row=row, column=6, value="") # Height ws1.cell(row=row, column=7, value="") # Weight ws1.cell(row=row, column=8, value="") # BMI auto-calculated c_bmi = ws1.cell(row=row, column=9) c_bmi.value = f"=IF(AND(H{row}<>\"\",G{row}<>\"\"),ROUND(H{row}/(G{row}/100)^2,1),\"\")" c_bmi.fill = PatternFill("solid", fgColor=COL_CALC) c_bmi.font = Font(size=9, name="Arial", color="444444") # Remaining columns for col in range(10, 17): ws1.cell(row=row, column=col, value="") ws1.row_dimensions[row].height = 16 # Add dropdowns dv_arm = add_dv_list(ws1, '"GT,ST"', f"D4:D23") dv_sex = add_dv_list(ws1, '"M,F,Other"', f"F4:F23") dv_ecog = add_dv_list(ws1, '"0,1,2,3,4"', f"J4:J23") dv_urban = add_dv_list(ws1, '"Urban,Peri-urban,Rural"', f"L4:L23") dv_ins = add_dv_list(ws1, '"Yes,No"', f"N4:N23") dv_ref = add_dv_list(ws1, '"OPD,IPD-Same Hospital,External Referral"', f"P4:P23") thin_border(ws1, 2, 1, 23, 16) # ═══════════════════════════════════════════════════════════════════ # SHEET 3 - MALIGNANCY & CHEMO # ═══════════════════════════════════════════════════════════════════ ws2 = wb.create_sheet("🩸 Malignancy_Chemo") ws2.sheet_properties.tabColor = "C55A11" col_w2 = [5, 14, 20, 22, 22, 18, 16, 20, 18, 20, 14, 14, 14, 14, 18, 18] for i, w in enumerate(col_w2, 1): ws2.column_dimensions[get_column_letter(i)].width = w hdr(ws2, 1, 1, "HEMATOLOGICAL MALIGNANCY & CHEMOTHERAPY DATA", bg="C55A11", fg="FFFFFF", bold=True, sz=13, merge_to=16) ws2.row_dimensions[1].height = 30 headers2 = [ "#", "Study ID", "Primary\nDiagnosis", "WHO/ICC 2022\nSubtype", "Key Molecular\nMarkers", "ELN Risk\n(AML)", "Disease\nStatus", "Chemotherapy\nRegimen", "Cycle\nNumber", "Last Chemo\nDate", "Days Chemo→\nFever", "G-CSF\nProphylaxis", "Prior HSCT", "Prior Lines\nof Therapy", "BM Biopsy\nBlasts%", "BM Biopsy\nDate" ] for col, h in enumerate(headers2, 1): c = ws2.cell(row=2, column=col, value=h) c.fill = PatternFill("solid", fgColor="C55A11") c.font = Font(bold=True, color="FFFFFF", size=9, name="Arial") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws2.row_dimensions[2].height = 32 for row in range(3, 23): ws2.cell(row=row, column=1, value=row-2) for col in range(2, 17): c = ws2.cell(row=row, column=col, value="") ws2.row_dimensions[row].height = 16 dv_dx = add_dv_list(ws2, '"AML,ALL,CML-Blast Crisis,CLL,DLBCL,HL,Multiple Myeloma,MDS,MDS/AML,HSCT Recipient,Other"', "C3:C22") dv_risk = add_dv_list(ws2, '"Favorable,Intermediate,Adverse,N/A"', "F3:F22") dv_status = add_dv_list(ws2, '"Newly Diagnosed-Induction,CR1,CR2,CR3,Partial Remission,Relapsed,Refractory,Post-HSCT"', "G3:G22") dv_gcsf = add_dv_list(ws2, '"Yes-Filgrastim,Yes-Pegfilgrastim,No"', "L3:L22") dv_hsct = add_dv_list(ws2, '"No,Yes-Autologous,Yes-Allogeneic-MRD,Yes-Allogeneic-MUD"', "M3:M22") thin_border(ws2, 2, 1, 22, 16) # ═══════════════════════════════════════════════════════════════════ # SHEET 4 - FN EPISODE # ═══════════════════════════════════════════════════════════════════ ws3 = wb.create_sheet("🌡️ FN_Episode") ws3.sheet_properties.tabColor = "FF0000" col_w3 = [5, 14, 16, 14, 14, 14, 14, 12, 12, 12, 12, 12, 12, 12, 20, 22, 20, 20] for i, w in enumerate(col_w3, 1): ws3.column_dimensions[get_column_letter(i)].width = w hdr(ws3, 1, 1, "FEBRILE NEUTROPENIA EPISODE — CLINICAL CHARACTERIZATION & MASCC SCORE", bg="C00000", fg="FFFFFF", bold=True, sz=13, merge_to=18) ws3.row_dimensions[1].height = 30 # MASCC score components header block hdr(ws3, 2, 1, "PATIENT ID", bg=COL_HEADER_MID, fg="FFFFFF", sz=9, merge_to=1) hdr(ws3, 2, 2, "Study ID", bg=COL_HEADER_MID, fg="FFFFFF", sz=9, merge_to=2) hdr(ws3, 2, 3, "FN DEFINITION", bg="C00000", fg="FFFFFF", sz=9, merge_to=5) hdr(ws3, 2, 6, "MASCC SCORE COMPONENTS", bg="843C0C", fg="FFFFFF", sz=9, merge_to=13) hdr(ws3, 2, 14, "MASCC TOTAL\n(AUTO)", bg=COL_CALC, fg="1F3864", sz=9) hdr(ws3, 2, 15, "CLINICAL SITE\nOF INFECTION", bg=COL_HEADER_MID, fg="FFFFFF", sz=9) hdr(ws3, 2, 16, "SEPSIS\n(Sepsis-3)", bg="C00000", fg="FFFFFF", sz=9) hdr(ws3, 2, 17, "MUCOSITIS\nGRADE (0-4)", bg=COL_HEADER_MID, fg="FFFFFF", sz=9) hdr(ws3, 2, 18, "CVC In Situ\n(Yes/No/Type)", bg=COL_HEADER_MID, fg="FFFFFF", sz=9) ws3.row_dimensions[2].height = 28 # Sub-headers row 3 subhdrs3 = [ "#", "Study ID", "Fever Onset\nDate", "Max Temp\n(°C)", "ANC at\nFever(/mm³)", "Fever\nPattern", "Burden\nIllness\n(5/3/0)", "No\nHypo\ntension(5)", "No\nCOPD\n(4)", "Solid/No\nFungal\n(4)", "No\nDehydr\n(3)", "Outp\ntient\n(3)", "Age\n<60\n(2)", "MASCC\nTOTAL", "Infection\nSite", "Sepsis\n(Y/N/Shock)", "Mucositis\nGrade", "CVC\nType" ] for col, h in enumerate(subhdrs3, 1): c = ws3.cell(row=3, column=col, value=h) c.fill = PatternFill("solid", fgColor=COL_HEADER_LIGHT) c.font = Font(bold=True, size=8, name="Arial", color="1F3864") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws3.row_dimensions[3].height = 40 for row in range(4, 24): ws3.cell(row=row, column=1, value=row-3) ws3.cell(row=row, column=2, value="") for col in range(3, 14): ws3.cell(row=row, column=col, value="") # MASCC auto total c_mascc = ws3.cell(row=row, column=14) c_mascc.value = f"=IF(G{row}=\"\",\"\",IFERROR(G{row}+H{row}+I{row}+J{row}+K{row}+L{row}+M{row},\"\"))" c_mascc.fill = PatternFill("solid", fgColor=COL_CALC) c_mascc.font = Font(bold=True, size=9, name="Arial", color="C00000") c_mascc.alignment = Alignment(horizontal="center", vertical="center") for col in range(15, 19): ws3.cell(row=row, column=col, value="") ws3.row_dimensions[row].height = 16 dv_fever_pat = add_dv_list(ws3, '"Continuous,Intermittent,Hectic"', "F4:F23") dv_burden = add_dv_list(ws3, '"5,3,0"', "G4:G23") dv_yn5 = add_dv_list(ws3, '"5,0"', "H4:H23") dv_yn4a = add_dv_list(ws3, '"4,0"', "I4:I23") dv_yn4b = add_dv_list(ws3, '"4,0"', "J4:J23") dv_yn3 = add_dv_list(ws3, '"3,0"', "K4:K23") dv_yn3b = add_dv_list(ws3, '"3,0"', "L4:L23") dv_yn2 = add_dv_list(ws3, '"2,0"', "M4:M23") dv_site = add_dv_list(ws3, '"No Focus-Primary Bacteremia,Pneumonia,UTI,CLABSI,Mucositis,Perianal/Typhlitis,Intra-abdominal,CNS,Sinusitis,Skin/Soft Tissue,Multiple Sites,Other"', "O4:O23") dv_sepsis = add_dv_list(ws3, '"No,Yes-Sepsis,Yes-Septic Shock"', "P4:P23") dv_muc = add_dv_list(ws3, '"0,1,2,3,4"', "Q4:Q23") dv_cvc = add_dv_list(ws3, '"No,PICC,Hickman,Port-a-cath,Temporary CVL"', "R4:R23") thin_border(ws3, 2, 1, 23, 18) # ═══════════════════════════════════════════════════════════════════ # SHEET 5 - LAB & MICROBIOLOGY (multi-timepoint) # ═══════════════════════════════════════════════════════════════════ ws4 = wb.create_sheet("🔬 Lab_Microbiology") ws4.sheet_properties.tabColor = "7030A0" col_w4 = [5, 14, 12, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 22, 22, 18, 18] for i, w in enumerate(col_w4, 1): ws4.column_dimensions[get_column_letter(i)].width = w hdr(ws4, 1, 1, "LABORATORY DATA — HEMATOLOGY | BIOCHEMISTRY | MICROBIOLOGY | INFLAMMATORY MARKERS", bg="7030A0", fg="FFFFFF", bold=True, sz=12, merge_to=22) ws4.row_dimensions[1].height = 28 # Section headers row 2 hdr(ws4, 2, 1, "ID", bg="7030A0", fg="FFFFFF", sz=9) hdr(ws4, 2, 2, "Study ID", bg="7030A0", fg="FFFFFF", sz=9) hdr(ws4, 2, 3, "TIMEPOINT", bg="7030A0", fg="FFFFFF", sz=9) hdr(ws4, 2, 4, "CBC / HEMATOLOGY", bg="1F3864", fg="FFFFFF", sz=9, merge_to=9) hdr(ws4, 2, 10, "BIOCHEMISTRY", bg="375623", fg="FFFFFF", sz=9, merge_to=14) hdr(ws4, 2, 15, "INFLAM. MARKERS", bg="843C0C", fg="FFFFFF", sz=9, merge_to=18) hdr(ws4, 2, 19, "MICROBIOLOGY", bg="C00000", fg="FFFFFF", sz=9, merge_to=22) ws4.row_dimensions[2].height = 22 # Column sub-headers row 3 subhdrs4 = [ "#", "Study ID", "Day/Timepoint", "WBC\n(/mm³)", "ANC\n(/mm³)", "Hgb\n(g/dL)", "Platelets\n(/mm³)", "Blasts\n(%PB)", "Bands\n(%)", "Retics\n(%)", "Cr\n(mg/dL)", "BUN\n(mg/dL)", "ALT\n(U/L)", "Total Bili\n(mg/dL)", "LDH\n(U/L)", "CRP\n(mg/L)", "PCT\n(ng/mL)", "Ferritin\n(ng/mL)", "Lactate\n(mmol/L)", "Blood Cx-1\nOrganism", "Blood Cx-2\nOrganism", "Galacto-\nmannan Index", "Beta-D\nGlucan(pg/mL)" ] for col, h in enumerate(subhdrs4, 1): c = ws4.cell(row=3, column=col, value=h) c.fill = PatternFill("solid", fgColor=COL_HEADER_LIGHT) c.font = Font(bold=True, size=8, name="Arial", color="1F3864") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws4.row_dimensions[3].height = 35 # Data rows - 7 timepoints per patient, 20 patients = 140 rows (truncate to 15 patients for usability) timepoints = ["Day 0 (Admission)", "Day 3", "Day 7", "Day 14", "Day 21", "Day 28", "At Defervescence", "At ANC Recovery", "At Discharge"] patient_count = 20 row_num = 4 for pt in range(1, patient_count + 1): for tp_i, tp in enumerate(timepoints): ws4.cell(row=row_num, column=1, value=pt if tp_i == 0 else "") ws4.cell(row=row_num, column=2, value="" if tp_i == 0 else "") ws4.cell(row=row_num, column=3, value=tp) # Color alternate patients bg_row = "F3E5F5" if pt % 2 == 0 else COL_WHITE for col in range(4, 23): c = ws4.cell(row=row_num, column=col, value="") c.fill = PatternFill("solid", fgColor=bg_row) ws4.row_dimensions[row_num].height = 14 row_num += 1 thin_border(ws4, 2, 1, row_num - 1, 22) # ═══════════════════════════════════════════════════════════════════ # SHEET 6 - ANTIBIOGRAM / ORGANISM DETAIL # ═══════════════════════════════════════════════════════════════════ ws5 = wb.create_sheet("🦠 Antibiogram") ws5.sheet_properties.tabColor = "FF0000" col_w5 = [5, 14, 16, 16, 14, 14, 14, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14] for i, w in enumerate(col_w5, 1): ws5.column_dimensions[get_column_letter(i)].width = w hdr(ws5, 1, 1, "MICROBIOLOGICAL CULTURE RESULTS & ANTIBIOGRAM", bg="C00000", fg="FFFFFF", bold=True, sz=13, merge_to=18) ws5.row_dimensions[1].height = 28 hdrs5 = [ "#", "Study ID", "Specimen\nType", "Collection\nDate", "Organism\nIsolated", "Gram\n+/-", "Days to\nPositivity", "Amox-Clav\n(S/R/I)", "Pip-Tazo\n(S/R/I)", "Cefepime\n(S/R/I)", "Meropenem\n(S/R/I)", "Cotrimox\n(S/R/I)", "Colistin\n(S/R/I)", "Vancomycin\n(S/R/I)", "ESBL\n(+/-)", "CRE\n(+/-)", "MRSA\n(+/-)", "MDR\n(Y/N)" ] for col, h in enumerate(hdrs5, 1): c = ws5.cell(row=2, column=col, value=h) c.fill = PatternFill("solid", fgColor="C00000") c.font = Font(bold=True, color="FFFFFF", size=9, name="Arial") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws5.row_dimensions[2].height = 35 for row in range(3, 43): ws5.cell(row=row, column=1, value=row-2) for col in range(2, 19): ws5.cell(row=row, column=col, value="") ws5.row_dimensions[row].height = 15 dv_spec = add_dv_list(ws5, '"Blood-Peripheral,Blood-CVC,Urine,Sputum,BAL,CSF,Wound Swab,Stool,Throat Swab,Fungal Culture"', "C3:C42") dv_gram = add_dv_list(ws5, '"Gram Positive,Gram Negative,Fungal,Anaerobe,Not done"', "F3:F42") for col_letter in ["H", "I", "J", "K", "L", "M", "N"]: add_dv_list(ws5, '"S,R,I,Not tested"', f"{col_letter}3:{col_letter}42") for col_letter in ["O", "P", "Q", "R"]: add_dv_list(ws5, '"Positive,Negative,Not done"', f"{col_letter}3:{col_letter}42") thin_border(ws5, 2, 1, 42, 18) # ═══════════════════════════════════════════════════════════════════ # SHEET 7 - GT TRANSFUSION LOG # ═══════════════════════════════════════════════════════════════════ ws6 = wb.create_sheet("💉 GT_Transfusion_Log") ws6.sheet_properties.tabColor = "00B050" col_w6 = [5, 14, 10, 14, 12, 12, 12, 14, 14, 12, 14, 14, 16, 16, 14, 14, 14, 14] for i, w in enumerate(col_w6, 1): ws6.column_dimensions[get_column_letter(i)].width = w hdr(ws6, 1, 1, "🟢 BUFFY COAT GRANULOCYTE TRANSFUSION LOG — GT ARM ONLY", bg="375623", fg="FFFFFF", bold=True, sz=13, merge_to=18) ws6.row_dimensions[1].height = 28 hdr(ws6, 2, 1, "GT ARM PATIENTS ONLY — Leave blank for ST arm", bg="E2EFDA", fg="375623", bold=True, sz=10, merge_to=18) ws6.row_dimensions[2].height = 18 hdrs6 = [ "#", "Study ID", "GT #\n(1-5)", "Date of\nTransfusion", "WBC Units\nPooled", "ABO/Rh\nProduct", "Granulocyte\nCount(×10¹⁰)", "Irradiation\nDose(Gy)", "Time Prep→\nTransfusion(h)", "Volume\n(mL)", "Dose\n(mL/kg)", "CMV\nStatus", "Cross-match\nCompatible", "Pre-med\nGiven(Y/N)", "Adverse\nEvent(Y/N)", "AE\nDescription", "Transfusion\nStopped(Y/N)", "ANC Post-GT\n(/mm³)" ] for col, h in enumerate(hdrs6, 1): c = ws6.cell(row=3, column=col, value=h) c.fill = PatternFill("solid", fgColor="375623") c.font = Font(bold=True, color="FFFFFF", size=9, name="Arial") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws6.row_dimensions[3].height = 35 for row in range(4, 54): ws6.cell(row=row, column=1, value=row-3) for col in range(2, 19): c = ws6.cell(row=row, column=col, value="") c.fill = PatternFill("solid", fgColor=COL_GT_ARM) ws6.row_dimensions[row].height = 15 dv_gtnum = add_dv_list(ws6, '"1,2,3,4,5"', "C4:C53") dv_cmv = add_dv_list(ws6, '"CMV Negative,CMV Positive,Unknown"', "L4:L53") dv_compat = add_dv_list(ws6, '"Compatible,Incompatible,Not done"', "M4:M53") for col_letter in ["N", "O", "Q"]: add_dv_list(ws6, '"Yes,No"', f"{col_letter}4:{col_letter}53") thin_border(ws6, 3, 1, 53, 18) # ═══════════════════════════════════════════════════════════════════ # SHEET 8 - TREATMENT # ═══════════════════════════════════════════════════════════════════ ws7 = wb.create_sheet("💊 Treatment") ws7.sheet_properties.tabColor = "00B0F0" col_w7 = [5, 14, 14, 16, 16, 14, 16, 14, 14, 14, 14, 14, 14, 12, 14, 14, 14, 14] for i, w in enumerate(col_w7, 1): ws7.column_dimensions[get_column_letter(i)].width = w hdr(ws7, 1, 1, "TREATMENT DATA — ANTIBIOTICS | ANTIFUNGALS | G-CSF | SUPPORTIVE CARE | ICU", bg="1F3864", fg="FFFFFF", bold=True, sz=13, merge_to=18) ws7.row_dimensions[1].height = 28 hdr(ws7, 2, 1, "ANTIBIOTIC", bg="1F3864", fg="FFFFFF", sz=9, merge_to=6) hdr(ws7, 2, 7, "ANTIFUNGAL", bg="375623", fg="FFFFFF", sz=9, merge_to=9) hdr(ws7, 2, 10, "G-CSF", bg="843C0C", fg="FFFFFF", sz=9, merge_to=12) hdr(ws7, 2, 13, "SUPPORTIVE CARE", bg="7030A0", fg="FFFFFF", sz=9, merge_to=15) hdr(ws7, 2, 16, "ICU / ORGAN SUPPORT", bg="C00000", fg="FFFFFF", sz=9, merge_to=18) ws7.row_dimensions[2].height = 18 hdrs7 = [ "#", "Study ID", "Time Fever→\n1st Abx(min)", "Empirical\nRegimen", "Antibiotic\nModified(Y/N)", "Total Abx\nDuration(d)", "Antifungal\nStarted(Y/N)", "Antifungal\nAgent", "Antifungal\nDuration(d)", "G-CSF\n(Y/N)", "G-CSF\nAgent", "G-CSF\nDoses", "pRBC\nUnits", "Platelets\nUnits", "TPN\n(Y/N)", "ICU\n(Y/N)", "Vasopressor\n(Y/N)", "Mech Vent\n(Y/N)" ] for col, h in enumerate(hdrs7, 1): c = ws7.cell(row=3, column=col, value=h) c.fill = PatternFill("solid", fgColor=COL_HEADER_LIGHT) c.font = Font(bold=True, size=9, name="Arial", color="1F3864") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws7.row_dimensions[3].height = 35 for row in range(4, 24): ws7.cell(row=row, column=1, value=row-3) for col in range(2, 19): ws7.cell(row=row, column=col, value="") ws7.row_dimensions[row].height = 15 dv_empreg = add_dv_list(ws7, '"Pip-Tazobactam,Cefepime,Meropenem,Imipenem,Combination:Pip-Tazo+Amikacin,Other"', "D4:D23") dv_af = add_dv_list(ws7, '"Fluconazole,Voriconazole,Caspofungin,Amphotericin B,Posaconazole"', "H4:H23") dv_gcsf2 = add_dv_list(ws7, '"Filgrastim,Pegfilgrastim,No"', "K4:K23") for col_letter in ["E", "G", "J", "O", "P", "Q", "R"]: add_dv_list(ws7, '"Yes,No"', f"{col_letter}4:{col_letter}23") thin_border(ws7, 2, 1, 23, 18) # ═══════════════════════════════════════════════════════════════════ # SHEET 9 - OUTCOMES # ═══════════════════════════════════════════════════════════════════ ws8 = wb.create_sheet("✅ Outcomes") ws8.sheet_properties.tabColor = "FF0000" col_w8 = [5, 14, 14, 16, 16, 14, 14, 16, 16, 14, 14, 14, 18, 18, 18] for i, w in enumerate(col_w8, 1): ws8.column_dimensions[get_column_letter(i)].width = w hdr(ws8, 1, 1, "PRIMARY & SECONDARY OUTCOMES — MORTALITY | ANC RECOVERY | DEFERVESCENCE | COST", bg="C00000", fg="FFFFFF", bold=True, sz=13, merge_to=15) ws8.row_dimensions[1].height = 28 hdr(ws8, 2, 1, "PRIMARY OUTCOME", bg="C00000", fg="FFFFFF", sz=9, merge_to=4) hdr(ws8, 2, 5, "SECONDARY OUTCOMES — TIME-TO-EVENT", bg="843C0C", fg="FFFFFF", sz=9, merge_to=10) hdr(ws8, 2, 11, "CLINICAL RESPONSE", bg="375623", fg="FFFFFF", sz=9, merge_to=12) hdr(ws8, 2, 13, "COST ANALYSIS (NPR)", bg="1F3864", fg="FFFFFF", sz=9, merge_to=15) ws8.row_dimensions[2].height = 18 hdrs8 = [ "#", "Study ID", "28-Day\nMortality\n(Alive/Dead)", "If Dead:\nCause of Death", "Days to\nANC≥500\n(from FN onset)", "ANC Recovery\nDate", "Days to\nDefervescence", "Defervescence\nDate", "Days to Cx\nClearance", "Total Abx\nDuration(d)", "Total Hospital\nStay(d)", "ICU\nDays", "Clinical Response\nDay 7", "Total Episode\nCost (NPR)", "GT Cost\n(NPR)" ] for col, h in enumerate(hdrs8, 1): c = ws8.cell(row=3, column=col, value=h) c.fill = PatternFill("solid", fgColor=COL_OUTCOME) c.font = Font(bold=True, size=9, name="Arial", color="1F3864") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws8.row_dimensions[3].height = 40 for row in range(4, 24): ws8.cell(row=row, column=1, value=row-3) for col in range(2, 16): c = ws8.cell(row=row, column=col, value="") c.fill = PatternFill("solid", fgColor="FFF2CC" if col in [14, 15] else COL_WHITE) ws8.row_dimensions[row].height = 15 dv_28d = add_dv_list(ws8, '"Alive,Dead"', "C4:C23") dv_cause = add_dv_list(ws8, '"Septic Shock,Respiratory Failure,MDR Infection,Disease Progression,GT Adverse Event,Unknown,N/A-Alive"', "D4:D23") dv_cr7 = add_dv_list(ws8, '"Complete Response,Partial Response,No Response,Progressive Disease"', "M4:M23") thin_border(ws8, 2, 1, 23, 15) # ═══════════════════════════════════════════════════════════════════ # SHEET 10 - FOLLOW UP # ═══════════════════════════════════════════════════════════════════ ws9 = wb.create_sheet("📅 Follow_Up") ws9.sheet_properties.tabColor = "00B050" col_w9 = [5, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 18, 20] for i, w in enumerate(col_w9, 1): ws9.column_dimensions[get_column_letter(i)].width = w hdr(ws9, 1, 1, "FOLLOW-UP DATA — DAY 30 / DAY 60 / DAY 90", bg="375623", fg="FFFFFF", bold=True, sz=13, merge_to=13) ws9.row_dimensions[1].height = 28 hdr(ws9, 2, 1, "", bg=COL_WHITE) hdr(ws9, 2, 2, "Study ID", bg=COL_HEADER_MID, fg="FFFFFF", sz=9) hdr(ws9, 2, 3, "DAY 30", bg="375623", fg="FFFFFF", sz=9, merge_to=5) hdr(ws9, 2, 6, "DAY 60", bg="375623", fg="FFFFFF", sz=9, merge_to=8) hdr(ws9, 2, 9, "DAY 90", bg="375623", fg="FFFFFF", sz=9, merge_to=11) hdr(ws9, 2, 12, "MALIGNANCY STATUS\nDAY 90", bg="843C0C", fg="FFFFFF", sz=9) hdr(ws9, 2, 13, "POST-GT\nALLOIMMUNIZATION", bg="7030A0", fg="FFFFFF", sz=9) ws9.row_dimensions[2].height = 28 subhdrs9 = [ "#", "Study ID", "D30 Status\n(Alive/Dead/LTFU)", "D30 Date", "Reason if Dead", "D60 Status", "D60 Date", "Notes", "D90 Status", "D90 Date", "Reason if Dead", "Disease Status\nD90", "HLA Antibody\n(Pos/Neg/ND)" ] for col, h in enumerate(subhdrs9, 1): c = ws9.cell(row=3, column=col, value=h) c.fill = PatternFill("solid", fgColor=COL_HEADER_LIGHT) c.font = Font(bold=True, size=9, name="Arial", color="1F3864") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws9.row_dimensions[3].height = 35 for row in range(4, 24): ws9.cell(row=row, column=1, value=row-3) for col in range(2, 14): ws9.cell(row=row, column=col, value="") ws9.row_dimensions[row].height = 15 for col_letter in ["C", "F", "I"]: add_dv_list(ws9, '"Alive,Dead,Lost to Follow-Up"', f"{col_letter}4:{col_letter}23") dv_ds90 = add_dv_list(ws9, '"Complete Remission,Partial Remission,Stable Disease,Progression,Relapse,Not assessed"', "L4:L23") dv_hla = add_dv_list(ws9, '"Positive,Negative,Not done"', "M4:M23") thin_border(ws9, 2, 1, 23, 13) # ═══════════════════════════════════════════════════════════════════ # SHEET 11 - SUMMARY DASHBOARD # ═══════════════════════════════════════════════════════════════════ ws10 = wb.create_sheet("📊 Summary_Dashboard") ws10.sheet_properties.tabColor = "FF9900" ws10.column_dimensions["A"].width = 35 ws10.column_dimensions["B"].width = 18 ws10.column_dimensions["C"].width = 18 ws10.column_dimensions["D"].width = 18 ws10.column_dimensions["E"].width = 25 hdr(ws10, 1, 1, "RESEARCH DASHBOARD — LIVE SUMMARY", bg="FF9900", fg="1F3864", bold=True, sz=14, merge_to=5) ws10.row_dimensions[1].height = 32 hdr(ws10, 2, 1, "VARIABLE", bg=COL_HEADER_MID, fg="FFFFFF", sz=10) hdr(ws10, 2, 2, "GT ARM", bg="375623", fg="FFFFFF", sz=10) hdr(ws10, 2, 3, "ST ARM", bg="843C0C", fg="FFFFFF", sz=10) hdr(ws10, 2, 4, "TOTAL", bg="1F3864", fg="FFFFFF", sz=10) hdr(ws10, 2, 5, "NOTES / INTERPRETATION", bg=COL_HEADER_LIGHT, fg="1F3864", sz=10) ws10.row_dimensions[2].height = 22 dash_data = [ ("Total patients enrolled", '=COUNTIF(\'👤 Patient_Demographics\'!D4:D23,"GT")', '=COUNTIF(\'👤 Patient_Demographics\'!D4:D23,"ST")', '=B3+C3', "Target: 30-40 per arm"), ("Male : Female ratio", "", "", "", "Calculate from Demographics sheet"), ("Mean age (years)", "", "", "", "Use AVERAGE() on Demographics col E"), ("AML patients (n)", "", "", "", "Count from Malignancy sheet"), ("ALL patients (n)", "", "", "", "Count from Malignancy sheet"), ("Mean MASCC score", "", "", "", "Use AVERAGE() on FN Episode col N"), ("High-risk FN (<21) n(%)", "", "", "", "MASCC<21 count"), ("Bacteremia rate n(%)", "", "", "", "Count positive blood cultures"), ("Gram-negative bacteremia n", "", "", "", "From Antibiogram sheet"), ("MDR organism n(%)", "", "", "", "From Antibiogram sheet - MDR=Yes"), ("28-day mortality n(%)", '=COUNTIFS(\'✅ Outcomes\'!C4:C23,"Dead",\'👤 Patient_Demographics\'!D4:D23,"GT")', '=COUNTIFS(\'✅ Outcomes\'!C4:C23,"Dead",\'👤 Patient_Demographics\'!D4:D23,"ST")', '=B14+C14', "PRIMARY OUTCOME"), ("Mean days to ANC recovery", "", "", "", "AVERAGE() from Outcomes col E"), ("Mean days to defervescence", "", "", "", "AVERAGE() from Outcomes col G"), ("Mean hospital stay (days)", "", "", "", "AVERAGE() from Outcomes col K"), ("ICU admission rate n(%)", "", "", "", "From Treatment sheet"), ("TRALI/adverse events n", "", "", "", "From GT Transfusion Log"), ("Mean GT cost per patient (NPR)", "", "", "", "From Outcomes col O"), ("Mean total cost per episode (NPR)", "", "", "", "From Outcomes col N"), ("30-day survival rate (%)", "", "", "", "From Follow-up sheet"), ("90-day survival rate (%)", "", "", "", "From Follow-up sheet"), ] for i, (label, gt_val, st_val, total_val, note) in enumerate(dash_data): r = 3 + i ws10.cell(row=r, column=1, value=label).font = Font(bold=True if label in ["28-day mortality n(%)", "Mean days to ANC recovery"] else False, size=10, name="Arial", color="1F3864") ws10.cell(row=r, column=1).fill = PatternFill("solid", fgColor=COL_HEADER_LIGHT if i % 2 == 0 else COL_WHITE) c2 = ws10.cell(row=r, column=2, value=gt_val) c2.fill = PatternFill("solid", fgColor="E2EFDA") c2.font = Font(size=10, name="Arial", color="375623", bold=True) c3 = ws10.cell(row=r, column=3, value=st_val) c3.fill = PatternFill("solid", fgColor="FFF2CC") c3.font = Font(size=10, name="Arial", color="843C0C", bold=True) c4 = ws10.cell(row=r, column=4, value=total_val) c4.fill = PatternFill("solid", fgColor=COL_CALC) c4.font = Font(size=10, name="Arial", bold=True) c5 = ws10.cell(row=r, column=5, value=note) c5.fill = PatternFill("solid", fgColor=COL_WHITE) c5.font = Font(italic=True, size=9, name="Arial", color="555555") ws10.row_dimensions[r].height = 16 thin_border(ws10, 2, 1, 22, 5) # ═══════════════════════════════════════════════════════════════════ # SHEET 12 - CODEBOOK # ═══════════════════════════════════════════════════════════════════ ws11 = wb.create_sheet("📝 Codebook") ws11.sheet_properties.tabColor = "AAAAAA" ws11.column_dimensions["A"].width = 5 ws11.column_dimensions["B"].width = 28 ws11.column_dimensions["C"].width = 20 ws11.column_dimensions["D"].width = 35 ws11.column_dimensions["E"].width = 20 ws11.column_dimensions["F"].width = 25 hdr(ws11, 1, 1, "CODEBOOK — VARIABLE DEFINITIONS, NORMAL RANGES & CODING GUIDE", bg="595959", fg="FFFFFF", bold=True, sz=13, merge_to=6) ws11.row_dimensions[1].height = 28 hdrs11 = ["#", "Variable Name", "Data Type", "Definition / Normal Range", "Code Values", "Sheet Location"] for col, h in enumerate(hdrs11, 1): c = ws11.cell(row=2, column=col, value=h) c.fill = PatternFill("solid", fgColor="595959") c.font = Font(bold=True, color="FFFFFF", size=10, name="Arial") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws11.row_dimensions[2].height = 22 codebook = [ ("FN Definition", "Clinical", "Fever ≥38.3°C once OR ≥38.0°C >1h + ANC <500/mm³", "As defined", "FN_Episode"), ("ANC", "Numeric (/mm³)", "Absolute Neutrophil Count = WBC × (Neut% + Band%)/100", "Normal: 1500-8000; Severe: <500; Profound: <100", "Lab_Microbiology"), ("MASCC Score", "Score (0-26)", "Multinational Association Supportive Care Cancer score", "≥21=Low Risk; <21=HIGH RISK", "FN_Episode"), ("CISNE Score", "Score (0-8)", "Clinical Index of Stable Febrile Neutropenia", "0=low risk; ≥3=high risk for complications", "FN_Episode"), ("PCT (Procalcitonin)", "Numeric (ng/mL)", "Bacteremia marker validated in Nepal (Shilpakar 2019)", "<0.5=unlikely bacteremia; 0.5-2=possible; >2=likely", "Lab_Microbiology"), ("CRP", "Numeric (mg/L)", "C-Reactive Protein", "Normal <10; Infection often >50", "Lab_Microbiology"), ("Galactomannan", "Index", "Aspergillus antigen", "Index >0.5=Positive; >1.0=Strongly positive", "Lab_Microbiology"), ("Beta-D-Glucan", "Numeric (pg/mL)", "Broad fungal marker (not specific for Cryptococcus/Mucoromycetes)", ">80=positive; >200=strongly positive", "Lab_Microbiology"), ("ESBL", "Y/N", "Extended-Spectrum Beta-Lactamase producing organism", "Positive/Negative/Not done", "Antibiogram"), ("CRE", "Y/N", "Carbapenem-Resistant Enterobacteriaceae", "Positive/Negative/Not done", "Antibiogram"), ("MRSA", "Y/N", "Methicillin-Resistant Staphylococcus aureus", "Positive/Negative/Not done", "Antibiogram"), ("MDR", "Y/N", "Multi-Drug Resistant: Resistant to ≥3 antibiotic classes", "Yes/No", "Antibiogram"), ("ECOG PS", "Score 0-4", "Eastern Cooperative Oncology Group Performance Status", "0=Normal; 1=Ambulatory; 2=<50% in bed; 3=>50% in bed; 4=Completely disabled", "Patient_Demographics"), ("GT Dose", "mL/kg", "Buffy coat granulocyte transfusion dose", "Target: 10 mL/kg per transfusion", "GT_Transfusion_Log"), ("Granulocyte Count", "×10¹⁰", "Final granulocyte count in buffy coat product", "Target: ≥1×10¹⁰ per transfusion", "GT_Transfusion_Log"), ("TRALI", "Clinical", "Transfusion-Related Acute Lung Injury", "New hypoxia + bilateral infiltrates within 6h of transfusion", "GT_Transfusion_Log"), ("DTP", "Minutes", "Differential Time to Positivity (CLABSI indicator)", "CVC positive ≥120 min before peripheral = CLABSI", "Lab_Microbiology"), ("28-day mortality", "Binary", "Death from any cause within 28 days of FN episode onset", "Alive/Dead — PRIMARY OUTCOME", "Outcomes"), ("ANC Recovery", "Days", "Days from FN onset to ANC ≥500 for 2 consecutive days", "Numeric; SECONDARY OUTCOME", "Outcomes"), ("Defervescence", "Days", "Days from FN onset to afebrile >24h without antipyretics", "Numeric; SECONDARY OUTCOME", "Outcomes"), ("ELN 2022 Risk", "Category", "European LeukemiaNet 2022 AML risk stratification", "Favorable/Intermediate/Adverse", "Malignancy_Chemo"), ("Clinical Response D7", "Category", "Response assessment at Day 7 of treatment", "CR=Afebrile+ANC recovering; PR=One criterion; NR=Neither; PD=Worsening", "Outcomes"), ("HLH Screen", "Panel", "Hemophagocytic Lymphohistiocytosis: Ferritin>10000, Triglycerides high, Fibrinogen low, D-dimer high", "Ferritin/Triglycerides/Fibrinogen/D-dimer from Lab sheet", "Lab_Microbiology"), ("Mucositis Grade", "WHO 0-4", "WHO Mucositis Scale", "0=None; 1=Soreness; 2=Erythema+Ulcers; 3=Ulcers+Liquid diet; 4=Alimentation impossible", "FN_Episode"), ("Sepsis-3 Criteria", "Clinical", "Suspected infection + SOFA increase ≥2", "SOFA score: Resp+Coag+Liver+CV+CNS+Renal", "FN_Episode"), ] for i, (var, dtype, defn, code, sheet) in enumerate(codebook): r = 3 + i ws11.cell(row=r, column=1, value=i+1) ws11.cell(row=r, column=2, value=var).font = Font(bold=True, size=9, name="Arial", color="1F3864") ws11.cell(row=r, column=3, value=dtype).font = Font(size=9, name="Arial") ws11.cell(row=r, column=4, value=defn).font = Font(size=9, name="Arial") ws11.cell(row=r, column=4).alignment = Alignment(wrap_text=True) ws11.cell(row=r, column=5, value=code).font = Font(size=9, name="Arial", color="C00000") ws11.cell(row=r, column=6, value=sheet).font = Font(size=9, name="Arial", color="2E75B6") bg = COL_HEADER_LIGHT if i % 2 == 0 else COL_WHITE for col in range(1, 7): ws11.cell(row=r, column=col).fill = PatternFill("solid", fgColor=bg) ws11.row_dimensions[r].height = 18 thin_border(ws11, 2, 1, 3 + len(codebook) - 1, 6) # ═══════════════════════════════════════════════════════════════════ # BUFFY COAT DIAGNOSTIC COMPARISON SHEET # ═══════════════════════════════════════════════════════════════════ ws12 = wb.create_sheet("🧫 Buffy_Coat_Diagnostic") ws12.sheet_properties.tabColor = "9900CC" col_w12 = [5, 14, 16, 16, 14, 14, 16, 16, 14, 14, 20, 14] for i, w in enumerate(col_w12, 1): ws12.column_dimensions[get_column_letter(i)].width = w hdr(ws12, 1, 1, "🧫 BUFFY COAT SMEAR — DIAGNOSTIC DATA vs BLOOD CULTURE COMPARISON (ALL PATIENTS)", bg="7030A0", fg="FFFFFF", bold=True, sz=13, merge_to=12) ws12.row_dimensions[1].height = 28 hdr(ws12, 2, 1, "BUFFY COAT SMEAR", bg="7030A0", fg="FFFFFF", sz=9, merge_to=7) hdr(ws12, 2, 8, "BLOOD CULTURE (REFERENCE)", bg="C00000", fg="FFFFFF", sz=9, merge_to=10) hdr(ws12, 2, 11, "CONCORDANCE", bg="375623", fg="FFFFFF", sz=9, merge_to=12) ws12.row_dimensions[2].height = 18 hdrs12 = [ "#", "Study ID", "Time Draw→\nSmear Result(h)", "Organisms\nVisualised(Y/N)", "Organism\nType on Smear", "Blast %\non Smear", "WBC Diff\nMatch Analyzer(Y/N)", "Blood Cx\nResult", "Blood Cx\nOrganism", "Days to\nCulture Result", "Concordance\nSmear vs Cx", "Time Saved\n(hours)" ] for col, h in enumerate(hdrs12, 1): c = ws12.cell(row=3, column=col, value=h) c.fill = PatternFill("solid", fgColor="F3E5F5") c.font = Font(bold=True, size=9, name="Arial", color="7030A0") c.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True) ws12.row_dimensions[3].height = 40 for row in range(4, 24): ws12.cell(row=row, column=1, value=row-3) for col in range(2, 11): ws12.cell(row=row, column=col, value="") # Concordance auto c_conc = ws12.cell(row=row, column=11) c_conc.value = f'=IF(OR(D{row}="",H{row}=""),"",IF(AND(D{row}="Yes",H{row}="Positive"),"True Positive",IF(AND(D{row}="No",H{row}="Negative"),"True Negative",IF(AND(D{row}="Yes",H{row}="Negative"),"False Positive","False Negative"))))' c_conc.fill = PatternFill("solid", fgColor=COL_CALC) c_conc.font = Font(size=9, name="Arial", bold=True, color="375623") # Time saved auto c_time = ws12.cell(row=row, column=12) c_time.value = f'=IF(AND(C{row}<>"",J{row}<>""),ROUND(J{row}*24-C{row},1),"")' c_time.fill = PatternFill("solid", fgColor=COL_CALC) c_time.font = Font(size=9, name="Arial", bold=True, color="375623") ws12.row_dimensions[row].height = 15 dv_org_vis = add_dv_list(ws12, '"Yes,No"', "D4:D23") dv_smear_org = add_dv_list(ws12, '"Gram-pos cocci,Gram-neg rods,Gram-neg cocci,Yeast forms,Leishmania amastigotes,Microfilariae,Multiple,None visualized"', "E4:E23") dv_match = add_dv_list(ws12, '"Yes,No,Not applicable"', "G4:G23") dv_cx_res = add_dv_list(ws12, '"Positive,Negative,Contaminated,Pending"', "H4:H23") thin_border(ws12, 2, 1, 23, 12) # ═══════════════════════════════════════════════════════════════════ # SAVE # ═══════════════════════════════════════════════════════════════════ output_path = "/home/daytona/workspace/fn-thesis/FN_HematMalig_DataEntry_CSH.xlsx" wb.save(output_path) print(f"SUCCESS: File saved to {output_path}") PYEOF

ls -la /home/daytona/workspace/fn-thesis/ && df -h /home/daytona/workspace/

mkdir -p /home/daytona/workspace/fn-thesis && ls -la /home/daytona/workspace/ && df -h /home/daytona/workspace/

python3 -c " import os os.makedirs('/home/daytona/workspace/fn-thesis', exist_ok=True) print('dir created:', os.path.isdir('/home/daytona/workspace/fn-thesis')) print('writable:', os.access('/home/daytona/workspace/fn-thesis', os.W_OK)) # test write with open('/home/daytona/workspace/fn-thesis/test.txt', 'w') as f: f.write('test') print('write test ok') os.remove('/home/daytona/workspace/fn-thesis/test.txt') "

python3 -c " import os, stat # find writable directory for p in ['/home/daytona', '/tmp', '/var/tmp']: if os.path.isdir(p) and os.access(p, os.W_OK): print('WRITABLE:', p) "

python3 << 'PYEOF' import openpyxl from openpyxl.styles import PatternFill, Font, Alignment, Border, Side from openpyxl.utils import get_column_letter from openpyxl.worksheet.datavalidation import DataValidation import os os.makedirs('/home/daytona/fn-thesis', exist_ok=True) wb = openpyxl.Workbook() # Colors C_NAVY = "1F3864" C_BLUE = "2E75B6" C_LBLUE = "BDD7EE" C_GREEN = "375623" C_LGREEN = "E2EFDA" C_RED = "C00000" C_ORANGE = "843C0C" C_CALC = "F2F2F2" C_REQ = "FFD7D7" C_WHITE = "FFFFFF" C_YELLOW = "FFF2CC" C_PURPLE = "7030A0" C_LPURP = "F3E5F5" def fill(color): return PatternFill("solid", fgColor=color) def fnt(bold=False, sz=9, color="000000", italic=False): return Font(name="Arial", size=sz, bold=bold, color=color, italic=italic) def aln(h="center", v="center", wrap=True): return Alignment(horizontal=h, vertical=v, wrap_text=wrap) def thin(): s = Side(style="thin", color="CCCCCC") return Border(left=s, right=s, top=s, bottom=s) def hdr(ws, r, c, txt, bg=C_BLUE, fg=C_WHITE, bold=True, sz=10, mc=None, rh=None): cell = ws.cell(row=r, column=c, value=txt) cell.fill = fill(bg); cell.font = fnt(bold=bold, sz=sz, color=fg) cell.alignment = aln(); cell.border = thin() if mc: ws.merge_cells(start_row=r, start_column=c, end_row=r, end_column=mc) if rh: ws.row_dimensions[r].height = rh return cell def lbl(ws, r, c, txt, bg=C_LBLUE, bold=False, sz=9): cell = ws.cell(row=r, column=c, value=txt) cell.fill = fill(bg); cell.font = fnt(bold=bold, sz=sz, color=C_NAVY) cell.alignment = aln(h="left"); cell.border = thin() return cell def inp(ws, r, c, val="", bg=C_WHITE, sz=9, bold=False, color="000000"): cell = ws.cell(row=r, column=c, value=val) cell.fill = fill(bg); cell.font = fnt(bold=bold, sz=sz, color=color) cell.alignment = aln(h="left"); cell.border = thin() return cell def formula(ws, r, c, f, bg=C_CALC, sz=9): cell = ws.cell(row=r, column=c, value=f) cell.fill = fill(bg); cell.font = fnt(sz=sz, color="444444") cell.alignment = aln(); cell.border = thin() return cell def dv_list(ws, opts, sq): dv = DataValidation(type="list", formula1=f'"{opts}"', allow_blank=True) dv.error = "Select from list"; dv.errorTitle = "Invalid" dv.showErrorMessage = True ws.add_data_validation(dv) dv.sqref = sq def set_cols(ws, widths): for i, w in enumerate(widths, 1): ws.column_dimensions[get_column_letter(i)].width = w # ═══════════════════════════════════════════════ # SHEET 1 — INSTRUCTIONS # ═══════════════════════════════════════════════ ws0 = wb.active ws0.title = "INSTRUCTIONS" ws0.sheet_properties.tabColor = C_NAVY set_cols(ws0, [4, 55, 35]) hdr(ws0,1,1,"FEBRILE NEUTROPENIA IN HEMATOLOGICAL MALIGNANCIES — DATA ENTRY WORKBOOK", bg=C_NAVY, sz=13, mc=3, rh=32) for r,t in [(2,"Civil Service Hospital, Kathmandu | DM Thesis — Clinical Hematology"), (3,"Study: Efficacy of Buffy Coat-Derived Granulocyte Transfusion in High-Risk FN"), (4,"Investigator: _______________________ Supervisor: _______________________"), (5,"IRC Approval No.: _______________ CTRI Registration No.: _______________")]: ws0.cell(row=r,column=2,value=t).font=fnt(bold=True,sz=10,color=C_NAVY) ws0.row_dimensions[r].height=16 hdr(ws0,7,1,"SHEET GUIDE",bg=C_BLUE,sz=11,mc=3,rh=22) guides=[ ("1. PATIENT_DEMOGRAPHICS","Age, sex, BMI, comorbidities, ECOG — 1 row per patient"), ("2. MALIGNANCY_CHEMO","Diagnosis, cytogenetics, regimen, disease status"), ("3. FN_EPISODE + MASCC","FN definition, MASCC score, clinical site of infection"), ("4. LAB_CBC_DAILY","Daily CBC — WBC, ANC, Hgb, Platelets, Blasts (fill each day row)"), ("5. LAB_BIOCHEM_MARKERS","Biochemistry, LFT, RFT, LDH, inflammatory markers — per timepoint"), ("6. MICROBIOLOGY","Blood cultures, organism, antibiogram, ESBL/CRE/MDR"), ("7. GT_TRANSFUSION_LOG","Buffy coat prep, dose, adverse events — GT arm patients only"), ("8. BUFFY_COAT_DIAGNOSTIC","Smear findings vs blood culture — ALL patients (key comparison)"), ("9. TREATMENT","Antibiotics, antifungals, G-CSF, ICU, vasopressors"), ("10. OUTCOMES","28-day mortality, ANC recovery, defervescence, costs"), ("11. FOLLOW_UP","Day 30/60/90 survival and disease status"), ("12. DASHBOARD","Auto-calculated summary — do not edit"), ("13. CODEBOOK","Variable definitions, codes, normal ranges"), ] for i,(s,d) in enumerate(guides): r=8+i ws0.cell(row=r,column=2,value=s).font=fnt(bold=True,sz=10,color=C_NAVY) ws0.cell(row=r,column=2).fill=fill(C_LBLUE) ws0.cell(row=r,column=3,value=d).font=fnt(sz=9) ws0.row_dimensions[r].height=15 hdr(ws0,22,1,"COLOUR CODE LEGEND",bg=C_NAVY,sz=11,mc=3,rh=22) legend=[(C_REQ,"RED = MANDATORY — must not be blank"), (C_CALC,"GREY = AUTO-CALCULATED — do not type"), (C_LGREEN,"GREEN = GT ARM ONLY — blank for ST patients"), (C_YELLOW,"YELLOW = COST / FINANCIAL DATA"), (C_LBLUE,"LIGHT BLUE = LABEL / HELPER ROW")] for i,(c,t) in enumerate(legend): r=23+i ws0.cell(row=r,column=2,value=t).font=fnt(sz=10,color=C_NAVY,bold=True) ws0.cell(row=r,column=2).fill=fill(c) ws0.row_dimensions[r].height=16 rules=["Enter all dates as DD/MM/YYYY", "Use dropdowns where provided — do NOT override with free text", "Negative / absent = 'No' or '0' — never leave blank", "Lab values: numbers only (units are in column header)", "Save file as CSH_FN_Data_[YourName].xlsx"] hdr(ws0,29,1,"RULES",bg=C_BLUE,sz=11,mc=3,rh=20) for i,r_txt in enumerate(rules): ws0.cell(row=30+i,column=2,value=r_txt).font=fnt(sz=9,color=C_NAVY) ws0.row_dimensions[30+i].height=14 # ═══════════════════════════════════════════════ # SHEET 2 — PATIENT DEMOGRAPHICS # ═══════════════════════════════════════════════ ws1 = wb.create_sheet("1.DEMOGRAPHICS") ws1.sheet_properties.tabColor = C_BLUE set_cols(ws1,[4,14,14,12,10,8,9,9,10,10,18,14,16,14,22,20]) hdr(ws1,1,1,"PATIENT DEMOGRAPHICS & BASELINE",bg=C_NAVY,sz=12,mc=16,rh=28) cols1=[("#",C_NAVY),("Study ID\n(MANDATORY)",C_RED),("Enroll\nDate",C_BLUE), ("Arm\nGT/ST",C_RED),("Age\n(yrs)",C_BLUE),("Sex",C_BLUE), ("Ht\n(cm)",C_BLUE),("Wt\n(kg)",C_BLUE),("BMI\n(auto)",C_CALC), ("ECOG\n(0-4)",C_BLUE),("District",C_BLUE),("Urban/\nRural",C_BLUE), ("Monthly\nIncome(NPR)",C_BLUE),("Insurance",C_BLUE), ("Comorbidities",C_BLUE),("Referral\nSource",C_BLUE)] for c,(h,bg) in enumerate(cols1,1): hdr(ws1,2,c,h,bg=bg,sz=9,rh=35) for row in range(3,23): ws1.cell(row=row,column=1,value=row-2).font=fnt(sz=9) inp(ws1,row,2,"",bg=C_REQ) # Study ID mandatory inp(ws1,row,3,"",bg=C_WHITE) inp(ws1,row,4,"",bg=C_REQ) # Arm mandatory for c in range(5,9): inp(ws1,row,c) formula(ws1,row,9,f'=IF(AND(H{row}<>"",G{row}<>""),ROUND(H{row}/(G{row}/100)^2,1),"")') for c in range(10,17): inp(ws1,row,c) ws1.row_dimensions[row].height=15 dv_list(ws1,'"GT,ST"','D3:D22') dv_list(ws1,'"M,F,Other"','F3:F22') dv_list(ws1,'"0,1,2,3,4"','J3:J22') dv_list(ws1,'"Urban,Peri-urban,Rural"','L3:L22') dv_list(ws1,'"Yes,No"','N3:N22') dv_list(ws1,'"OPD,Same Hospital IPD,External Referral"','P3:P22') # ═══════════════════════════════════════════════ # SHEET 3 — MALIGNANCY & CHEMO # ═══════════════════════════════════════════════ ws2 = wb.create_sheet("2.MALIGNANCY_CHEMO") ws2.sheet_properties.tabColor = "C55A11" set_cols(ws2,[4,14,20,22,22,16,18,20,10,14,12,14,16,14,14,14]) hdr(ws2,1,1,"HEMATOLOGICAL MALIGNANCY & CHEMOTHERAPY",bg="C55A11",sz=12,mc=16,rh=28) hdrs2=["#","Study ID","Primary Diagnosis","WHO/ICC 2022\nSubtype", "Key Molecular\nMarkers","ELN 2022\nRisk","Disease\nStatus", "Chemo\nRegimen","Cycle\n#","Last Chemo\nDate", "Days Chemo\n→Fever","G-CSF\nProphylaxis", "Prior HSCT","Prior Lines\nof Therapy","BM Blasts\n(%)","BM Biopsy\nDate"] for c,h in enumerate(hdrs2,1): hdr(ws2,2,c,h,bg="C55A11",sz=9,rh=35) for row in range(3,23): ws2.cell(row=row,column=1,value=row-2).font=fnt(sz=9) inp(ws2,row,2,"",bg=C_REQ) for c in range(3,17): inp(ws2,row,c) ws2.row_dimensions[row].height=15 dv_list(ws2,'"AML,ALL,CML-Blast Crisis,CLL,DLBCL,Hodgkin Lymphoma,Multiple Myeloma,MDS,MDS/AML,HSCT Recipient,Other"','C3:C22') dv_list(ws2,'"Favorable,Intermediate,Adverse,N/A"','F3:F22') dv_list(ws2,'"Newly Diagnosed-Induction,CR1,CR2,CR3,Partial Remission,Relapsed,Refractory,Post-HSCT"','G3:G22') dv_list(ws2,'"Yes-Filgrastim,Yes-Pegfilgrastim,No"','L3:L22') dv_list(ws2,'"No,Yes-Autologous,Yes-Allogeneic-MRD,Yes-Allogeneic-MUD"','M3:M22') # ═══════════════════════════════════════════════ # SHEET 4 — FN EPISODE + MASCC # ═══════════════════════════════════════════════ ws3 = wb.create_sheet("3.FN_EPISODE+MASCC") ws3.sheet_properties.tabColor = C_RED set_cols(ws3,[4,14,14,12,12,12,10,10,10,10,10,10,10,13,18,16,12,16]) hdr(ws3,1,1,"FN EPISODE CHARACTERIZATION + MASCC SCORE (AUTO-CALCULATED)",bg=C_RED,sz=12,mc=18,rh=28) hdr(ws3,2,1,"PATIENT",bg=C_NAVY,sz=9,mc=2) hdr(ws3,2,3,"FN DEFINITION",bg=C_RED,sz=9,mc=5) hdr(ws3,2,8,"MASCC SCORE — Enter points per component",bg="843C0C",sz=9,mc=13) hdr(ws3,2,14,"MASCC\nTOTAL",bg=C_CALC,fg=C_NAVY,sz=9) hdr(ws3,2,15,"INFECTION\nSITE",bg=C_BLUE,sz=9) hdr(ws3,2,16,"SEPSIS\n(Sepsis-3)",bg=C_RED,sz=9) hdr(ws3,2,17,"MUCOSITIS\nGRADE",bg=C_BLUE,sz=9) hdr(ws3,2,18,"CVC IN\nSITU",bg=C_BLUE,sz=9) ws3.row_dimensions[2].height=22 sh3=["#","Study ID", "Fever Onset\nDate","Max Temp\n(°C)","ANC at\nFever(/mm³)","Fever\nPattern", "Burden\nIllness\n(5/3/0)","No Hypo-\ntension\n(5/0)","No\nCOPD\n(4/0)", "Solid/No\nFungal\n(4/0)","No Dehy-\ndration\n(3/0)","Out-\npatient\n(3/0)","Age\n<60\n(2/0)", "MASCC\nTOTAL","Infection\nSite","Sepsis-3\nStatus","Mucositis\nGrade","CVC\nType"] for c,h in enumerate(sh3,1): hdr(ws3,3,c,h,bg=C_LBLUE,fg=C_NAVY,sz=8,rh=40) for row in range(4,24): ws3.cell(row=row,column=1,value=row-3).font=fnt(sz=9) inp(ws3,row,2,"",bg=C_REQ) for c in range(3,14): inp(ws3,row,c) formula(ws3,row,14, f'=IF(G{row}="","",IFERROR(G{row}+H{row}+I{row}+J{row}+K{row}+L{row}+M{row},""))', bg="FFE0E0") ws3.cell(row=row,column=14).font=fnt(bold=True,sz=10,color=C_RED) for c in range(15,19): inp(ws3,row,c) ws3.row_dimensions[row].height=16 dv_list(ws3,'"Continuous,Intermittent,Hectic,Sustained"','F4:F23') dv_list(ws3,'"5,3,0"','G4:G23') for col in ['H','I','J']: dv_list(ws3,f'"5,0"' if col=='H' else '"4,0"',f'{col}4:{col}23') dv_list(ws3,'"3,0"','K4:K23') dv_list(ws3,'"3,0"','L4:L23') dv_list(ws3,'"2,0"','M4:M23') dv_list(ws3,'"No Focus-Primary Bacteremia,Pneumonia,UTI,CLABSI,Mucositis/Oropharyngeal,Perianal/Typhlitis,Sinusitis-Fungal,Skin/Soft Tissue,CNS,Intra-abdominal,Multiple,Other"','O4:O23') dv_list(ws3,'"No,Yes-Sepsis,Yes-Septic Shock"','P4:P23') dv_list(ws3,'"0,1,2,3,4"','Q4:Q23') dv_list(ws3,'"No,PICC,Hickman,Port-a-cath,Temporary CVL"','R4:R23') # ═══════════════════════════════════════════════ # SHEET 5 — DAILY CBC # ═══════════════════════════════════════════════ ws4 = wb.create_sheet("4.LAB_CBC_DAILY") ws4.sheet_properties.tabColor = "375623" set_cols(ws4,[4,14,14,10,10,10,10,10,10,10,10]) hdr(ws4,1,1,"DAILY CBC — COMPLETE BLOOD COUNT (1 ROW PER PATIENT PER TIMEPOINT)",bg=C_NAVY,sz=12,mc=11,rh=28) hdr(ws4,2,1,"ENTER ONE ROW PER DAY/TIMEPOINT — Use dropdown for Timepoint",bg=C_LGREEN,fg=C_GREEN,sz=10,mc=11,rh=18) sh4=["#","Study ID","Timepoint","Date","WBC\n(/mm³)","ANC\n(/mm³)","Hgb\n(g/dL)","Platelets\n(/mm³)","Blasts\n(%PB)","Bands\n(%)","Retics\n(%)"] for c,h in enumerate(sh4,1): hdr(ws4,3,c,h,bg=C_GREEN,fg=C_WHITE,sz=9,rh=32) timepoints=["Day 0-Admission","Day 1","Day 2","Day 3","Day 4","Day 5","Day 6","Day 7","Day 10","Day 14","Day 21","Day 28","At Defervescence","At ANC Recovery","At Discharge"] tp_str=",".join(timepoints) row=4; pt=1 for p in range(1,21): for i,tp in enumerate(timepoints): ws4.cell(row=row,column=1,value=p if i==0 else "").font=fnt(sz=9) inp(ws4,row,2,"" if i>0 else "",bg=C_REQ if i==0 else C_WHITE) inp(ws4,row,3,tp) for c in range(4,12): bg = "F0FFF0" if row%2==0 else C_WHITE inp(ws4,row,c,bg=bg) ws4.row_dimensions[row].height=13 row+=1 dv_list(ws4,f'"{tp_str}"',f'C4:C{row-1}') # ═══════════════════════════════════════════════ # SHEET 6 — BIOCHEM & INFLAMMATORY MARKERS # ═══════════════════════════════════════════════ ws5 = wb.create_sheet("5.LAB_BIOCHEM_MARKERS") ws5.sheet_properties.tabColor = "843C0C" set_cols(ws5,[4,14,14,10,10,10,12,12,12,12,12,12,12,14,14,14,14]) hdr(ws5,1,1,"BIOCHEMISTRY + INFLAMMATORY MARKERS (per timepoint)",bg="843C0C",sz=12,mc=17,rh=28) hdr(ws5,2,1,"RENAL/HEPATIC",bg="843C0C",fg=C_WHITE,sz=9,mc=7) hdr(ws5,2,8,"COAGULATION/OTHER",bg=C_NAVY,fg=C_WHITE,sz=9,mc=11) hdr(ws5,2,12,"INFLAMMATORY MARKERS",bg=C_RED,fg=C_WHITE,sz=9,mc=15) hdr(ws5,2,16,"FUNGAL",bg=C_PURPLE,fg=C_WHITE,sz=9,mc=17) ws5.row_dimensions[2].height=18 sh5=["#","Study ID","Timepoint","Creat\n(mg/dL)","BUN\n(mg/dL)","ALT\n(U/L)","Total Bili\n(mg/dL)", "LDH\n(U/L)","Fibrinogen\n(mg/dL)","D-dimer\n(mg/L)","INR","Lactate\n(mmol/L)", "CRP\n(mg/L)","PCT\n(ng/mL)","Ferritin\n(ng/mL)","Triglyc\n(mg/dL)", "Galacto-\nmannan","Beta-D\nGlucan\n(pg/mL)"] for c,h in enumerate(sh5,1): hdr(ws5,3,c,h,bg=C_LBLUE,fg=C_NAVY,sz=8,rh=38) tps5=["Day 0-Admission","Day 3","Day 7","Day 14","At Defervescence","At Discharge"] row=4 for p in range(1,21): for i,tp in enumerate(tps5): ws5.cell(row=row,column=1,value=p if i==0 else "").font=fnt(sz=9) inp(ws5,row,2,"",bg=C_REQ if i==0 else C_WHITE) inp(ws5,row,3,tp) for c in range(4,19): bg = "FFF8F0" if row%2==0 else C_WHITE inp(ws5,row,c,bg=bg) ws5.row_dimensions[row].height=13 row+=1 dv_list(ws5,f'"{",".join(tps5)}"',f'C4:C{row-1}') # ═══════════════════════════════════════════════ # SHEET 7 — MICROBIOLOGY + ANTIBIOGRAM # ═══════════════════════════════════════════════ ws6 = wb.create_sheet("6.MICROBIOLOGY") ws6.sheet_properties.tabColor = C_RED set_cols(ws6,[4,14,16,14,18,14,12,12,12,12,12,12,12,12,14,14,14,12]) hdr(ws6,1,1,"MICROBIOLOGY — CULTURE RESULTS & ANTIBIOGRAM",bg=C_RED,sz=12,mc=18,rh=28) hdr(ws6,2,1,"ISOLATE DETAILS",bg=C_RED,fg=C_WHITE,sz=9,mc=7) hdr(ws6,2,8,"ANTIBIOTIC SENSITIVITY (S=Sensitive R=Resistant I=Intermediate)",bg=C_NAVY,fg=C_WHITE,sz=9,mc=14) hdr(ws6,2,15,"RESISTANCE\nPATTERN",bg=C_ORANGE,fg=C_WHITE,sz=9,mc=18) ws6.row_dimensions[2].height=22 sh6=["#","Study ID","Specimen","Culture\nDate","Organism\nIsolated","Gram +/-", "Days to\nPositivity", "Pip-Tazo","Cefepime","Meropenem","Gentamicin","Amikacin","Cotrimox","Vancomycin", "ESBL","CRE","MRSA","MDR\n(Y/N)"] for c,h in enumerate(sh6,1): hdr(ws6,3,c,h,bg=C_RED if c<=7 else (C_NAVY if c<=14 else C_ORANGE),fg=C_WHITE,sz=8,rh=38) for row in range(4,44): ws6.cell(row=row,column=1,value=row-3).font=fnt(sz=9) inp(ws6,row,2,"",bg=C_REQ) for c in range(3,19): inp(ws6,row,c) ws6.row_dimensions[row].height=14 dv_list(ws6,'"Blood-Peripheral,Blood-CVC,Urine,Sputum,BAL,CSF,Wound Swab,Stool,Fungal Culture"','C4:C43') dv_list(ws6,'"Gram Positive,Gram Negative,Fungal,Anaerobe"','F4:F43') for col in ['H','I','J','K','L','M','N']: dv_list(ws6,'"S,R,I,Not tested"',f'{col}4:{col}43') for col in ['O','P','Q']: dv_list(ws6,'"Positive,Negative,Not done"',f'{col}4:{col}43') dv_list(ws6,'"Yes,No"','R4:R43') # ═══════════════════════════════════════════════ # SHEET 8 — GT TRANSFUSION LOG # ═══════════════════════════════════════════════ ws7 = wb.create_sheet("7.GT_TRANSFUSION_LOG") ws7.sheet_properties.tabColor = "00B050" set_cols(ws7,[4,14,8,14,10,12,14,10,12,10,10,12,14,12,14,18,12,12]) hdr(ws7,1,1,"GT TRANSFUSION LOG — BUFFY COAT — GT ARM PATIENTS ONLY",bg=C_GREEN,sz=12,mc=18,rh=28) hdr(ws7,2,1,"GT ARM PATIENTS ONLY — Leave entirely blank for ST arm",bg=C_LGREEN,fg=C_GREEN,sz=10,mc=18,rh=18) hdr(ws7,3,1,"PREP DETAILS",bg=C_GREEN,fg=C_WHITE,sz=9,mc=9) hdr(ws7,3,10,"TRANSFUSION",bg="1E6E42",fg=C_WHITE,sz=9,mc=14) hdr(ws7,3,15,"ADVERSE EVENTS",bg=C_RED,fg=C_WHITE,sz=9,mc=18) ws7.row_dimensions[3].height=18 sh7=["#","Study ID","GT\n#","Prep\nDate","WB Units\nPooled","Final Gran\nCount(×10¹⁰)","Irrad\nDose(Gy)","Time Prep\n→Transfusion(h)","ABO/Rh\nProduct", "Volume\n(mL)","Dose\n(mL/kg)","CMV\nStatus","Cross-match","Pre-med\nGiven", "AE\n(Y/N)","AE\nDescription","Transfusion\nStopped(Y/N)","ANC Post-GT(/mm³)"] for c,h in enumerate(sh7,1): hdr(ws7,4,c,h,bg=C_GREEN if c<=9 else ("1E6E42" if c<=14 else C_RED),fg=C_WHITE,sz=8,rh=38) for row in range(5,55): ws7.cell(row=row,column=1,value=row-4).font=fnt(sz=9) for c in range(2,19): inp(ws7,row,c,bg=C_LGREEN) ws7.row_dimensions[row].height=14 dv_list(ws7,'"1,2,3,4,5"','C5:C54') dv_list(ws7,'"CMV Negative,CMV Positive,Unknown"','L5:L54') dv_list(ws7,'"Compatible,Incompatible,Not done"','M5:M54') for col in ['N','O','Q']: dv_list(ws7,'"Yes,No"',f'{col}5:{col}54') # ═══════════════════════════════════════════════ # SHEET 9 — BUFFY COAT DIAGNOSTIC COMPARISON # ═══════════════════════════════════════════════ ws8 = wb.create_sheet("8.BUFFY_COAT_DIAGNOSTIC") ws8.sheet_properties.tabColor = C_PURPLE set_cols(ws8,[4,14,14,14,22,12,14,16,18,14,16,12]) hdr(ws8,1,1,"BUFFY COAT SMEAR vs BLOOD CULTURE — DIAGNOSTIC COMPARISON — ALL PATIENTS",bg=C_PURPLE,sz=12,mc=12,rh=28) hdr(ws8,2,1,"BUFFY COAT SMEAR FINDINGS",bg=C_PURPLE,fg=C_WHITE,sz=9,mc=7) hdr(ws8,2,8,"BLOOD CULTURE (REFERENCE STANDARD)",bg=C_RED,fg=C_WHITE,sz=9,mc=10) hdr(ws8,2,11,"AUTO-ANALYSIS",bg=C_CALC,fg=C_NAVY,sz=9,mc=12) ws8.row_dimensions[2].height=18 sh8=["#","Study ID","Time Draw→\nSmear Result(h)","Organisms\nSeen (Y/N)","Organism\nType on Smear", "Blast%\non Smear","WBC Diff Matches\nAnalyzer(Y/N)", "Cx Result\n(+/-)","Organism\nIdentified","Days to Cx\nResult", "Concordance\n(Auto)","Time Saved\n(hours, Auto)"] for c,h in enumerate(sh8,1): hdr(ws8,3,c,h,bg=C_PURPLE if c<=7 else (C_RED if c<=10 else C_CALC), fg=C_WHITE if c!=11 else C_NAVY,sz=8,rh=40) for row in range(4,24): ws8.cell(row=row,column=1,value=row-3).font=fnt(sz=9) inp(ws8,row,2,"",bg=C_REQ) for c in range(3,11): inp(ws8,row,c,bg=C_LPURP) # Concordance auto formula(ws8,row,11, f'=IF(OR(D{row}="",H{row}=""),"",IF(AND(D{row}="Yes",H{row}="Positive"),"True Positive",IF(AND(D{row}="No",H{row}="Negative"),"True Negative",IF(AND(D{row}="Yes",H{row}="Negative"),"False Positive","False Negative"))))') ws8.cell(row=row,column=11).font=fnt(bold=True,sz=9,color=C_GREEN) # Time saved auto formula(ws8,row,12, f'=IF(AND(C{row}<>"",J{row}<>""),ROUND(J{row}*24-C{row},1),"")') ws8.cell(row=row,column=12).font=fnt(bold=True,sz=9,color=C_NAVY) ws8.row_dimensions[row].height=15 dv_list(ws8,'"Yes,No"','D4:D23') dv_list(ws8,'"Gram-pos cocci,Gram-neg rods,Gram-neg cocci,Yeast forms,Leishmania amastigotes,Microfilariae,Mixed,None visualized"','E4:E23') dv_list(ws8,'"Yes,No,Not applicable"','G4:G23') dv_list(ws8,'"Positive,Negative,Contaminated,Pending"','H4:H23') # ═══════════════════════════════════════════════ # SHEET 10 — TREATMENT # ═══════════════════════════════════════════════ ws9 = wb.create_sheet("9.TREATMENT") ws9.sheet_properties.tabColor = "00B0F0" set_cols(ws9,[4,14,16,18,14,12,14,16,12,12,14,12,10,10,12,12,12,12]) hdr(ws9,1,1,"TREATMENT — ANTIBIOTICS | ANTIFUNGALS | G-CSF | ICU SUPPORT",bg=C_NAVY,sz=12,mc=18,rh=28) hdr(ws9,2,1,"ANTIBIOTICS",bg=C_NAVY,fg=C_WHITE,sz=9,mc=6) hdr(ws9,2,7,"ANTIFUNGALS",bg=C_GREEN,fg=C_WHITE,sz=9,mc=9) hdr(ws9,2,10,"G-CSF",bg="843C0C",fg=C_WHITE,sz=9,mc=12) hdr(ws9,2,13,"TRANSFUSION SUPPORT",bg=C_BLUE,fg=C_WHITE,sz=9,mc=15) hdr(ws9,2,16,"ICU & ORGAN SUPPORT",bg=C_RED,fg=C_WHITE,sz=9,mc=18) ws9.row_dimensions[2].height=18 sh9=["#","Study ID", "Time Fever→\n1st Abx(min)","Empirical\nRegimen","Abx\nModified(Y/N)","Total Abx\nDuration(d)", "Antifungal\n(Y/N)","Antifungal\nAgent","AF Duration\n(d)", "G-CSF(Y/N)","G-CSF Agent","G-CSF\nDoses", "pRBC\nUnits","Platelets\nUnits","TPN(Y/N)", "ICU(Y/N)","Vasopressor\n(Y/N)","Mech Vent\n(Y/N)"] for c,h in enumerate(sh9,1): bg = C_NAVY if c<=6 else (C_GREEN if c<=9 else ("843C0C" if c<=12 else (C_BLUE if c<=15 else C_RED))) hdr(ws9,3,c,h,bg=bg,fg=C_WHITE,sz=8,rh=38) for row in range(4,24): ws9.cell(row=row,column=1,value=row-3).font=fnt(sz=9) inp(ws9,row,2,"",bg=C_REQ) for c in range(3,19): inp(ws9,row,c) ws9.row_dimensions[row].height=15 dv_list(ws9,'"Pip-Tazobactam,Cefepime,Meropenem,Imipenem,Pip-Tazo+Amikacin,Other"','D4:D23') dv_list(ws9,'"Fluconazole,Voriconazole,Caspofungin,Amphotericin B,Posaconazole"','H4:H23') dv_list(ws9,'"Filgrastim,Pegfilgrastim"','K4:K23') for col in ['E','G','J','O','P','Q','R']: dv_list(ws9,'"Yes,No"',f'{col}4:{col}23') # ═══════════════════════════════════════════════ # SHEET 11 — OUTCOMES # ═══════════════════════════════════════════════ ws10 = wb.create_sheet("10.OUTCOMES") ws10.sheet_properties.tabColor = C_RED set_cols(ws10,[4,14,16,22,14,14,14,14,14,14,14,12,18,18,18]) hdr(ws10,1,1,"PRIMARY & SECONDARY OUTCOMES",bg=C_RED,sz=12,mc=15,rh=28) hdr(ws10,2,1,"PRIMARY",bg=C_RED,fg=C_WHITE,sz=9,mc=4) hdr(ws10,2,5,"SECONDARY — TIME-TO-EVENT",bg="843C0C",fg=C_WHITE,sz=9,mc=12) hdr(ws10,2,13,"COST ANALYSIS (NPR)",bg=C_NAVY,fg=C_WHITE,sz=9,mc=15) ws10.row_dimensions[2].height=18 sh10=["#","Study ID","28-Day\nMortality","Cause of\nDeath (if dead)", "Days to\nANC≥500","ANC Recovery\nDate","Days to\nDefervescence", "Defervescence\nDate","Days to Cx\nClearance","Abx Duration\n(d)", "Hospital Stay\n(d)","ICU Days", "Day-7 Clinical\nResponse","Total Episode\nCost (NPR)","GT Product\nCost (NPR)"] for c,h in enumerate(sh10,1): hdr(ws10,3,c,h,bg=C_RED if c<=4 else ("843C0C" if c<=12 else C_NAVY),fg=C_WHITE,sz=8,rh=40) for row in range(4,24): ws10.cell(row=row,column=1,value=row-3).font=fnt(sz=9) inp(ws10,row,2,"",bg=C_REQ) for c in range(3,13): inp(ws10,row,c) for c in range(13,16): inp(ws10,row,c,bg=C_YELLOW) ws10.row_dimensions[row].height=15 dv_list(ws10,'"Alive,Dead"','C4:C23') dv_list(ws10,'"Septic Shock,Respiratory Failure,MDR Infection,Disease Progression,GT Adverse Event,Unknown,N/A-Alive"','D4:D23') dv_list(ws10,'"Complete Response,Partial Response,No Response,Progressive Disease"','M4:M23') # ═══════════════════════════════════════════════ # SHEET 12 — FOLLOW UP # ═══════════════════════════════════════════════ ws11 = wb.create_sheet("11.FOLLOW_UP") ws11.sheet_properties.tabColor = C_GREEN set_cols(ws11,[4,14,18,12,18,18,12,18,18,12,18,20,18]) hdr(ws11,1,1,"FOLLOW-UP — DAY 30 / 60 / 90",bg=C_GREEN,sz=12,mc=13,rh=28) hdr(ws11,2,3,"DAY 30",bg=C_GREEN,fg=C_WHITE,sz=9,mc=5) hdr(ws11,2,6,"DAY 60",bg="1E6E42",fg=C_WHITE,sz=9,mc=8) hdr(ws11,2,9,"DAY 90",bg=C_GREEN,fg=C_WHITE,sz=9,mc=11) hdr(ws11,2,12,"DISEASE STATUS D90",bg="843C0C",fg=C_WHITE,sz=9) hdr(ws11,2,13,"POST-GT HLA Ab",bg=C_PURPLE,fg=C_WHITE,sz=9) ws11.row_dimensions[2].height=22 sh11=["#","Study ID", "D30 Status","D30 Date","Reason if Dead", "D60 Status","D60 Date","Reason if Dead", "D90 Status","D90 Date","Reason if Dead", "Disease Status D90","HLA Ab (Post-GT)"] for c,h in enumerate(sh11,1): bg = C_GREEN if c in [3,4,5] else ("1E6E42" if c in [6,7,8] else (C_GREEN if c in [9,10,11] else ("843C0C" if c==12 else C_PURPLE))) hdr(ws11,3,c,h,bg=bg if c>2 else C_BLUE,fg=C_WHITE,sz=9,rh=32) for row in range(4,24): ws11.cell(row=row,column=1,value=row-3).font=fnt(sz=9) inp(ws11,row,2,"",bg=C_REQ) for c in range(3,14): inp(ws11,row,c,bg=C_LGREEN) ws11.row_dimensions[row].height=15 for col in ['C','F','I']: dv_list(ws11,'"Alive,Dead,Lost to Follow-Up"',f'{col}4:{col}23') dv_list(ws11,'"Complete Remission,Partial Remission,Stable Disease,Progression,Relapse,Not assessed"','L4:L23') dv_list(ws11,'"Positive,Negative,Not done"','M4:M23') # ═══════════════════════════════════════════════ # SHEET 13 — DASHBOARD # ═══════════════════════════════════════════════ ws12 = wb.create_sheet("12.DASHBOARD") ws12.sheet_properties.tabColor = "FF9900" ws12.column_dimensions["A"].width = 38 ws12.column_dimensions["B"].width = 16 ws12.column_dimensions["C"].width = 16 ws12.column_dimensions["D"].width = 16 ws12.column_dimensions["E"].width = 28 hdr(ws12,1,1,"RESEARCH DASHBOARD — LIVE AUTO-SUMMARY",bg="FF9900",fg=C_NAVY,sz=14,mc=5,rh=32) hdr(ws12,2,1,"METRIC",bg=C_NAVY,fg=C_WHITE,sz=10) hdr(ws12,2,2,"GT ARM",bg=C_GREEN,fg=C_WHITE,sz=10) hdr(ws12,2,3,"ST ARM",bg="843C0C",fg=C_WHITE,sz=10) hdr(ws12,2,4,"TOTAL",bg=C_NAVY,fg=C_WHITE,sz=10) hdr(ws12,2,5,"NOTES",bg=C_LBLUE,fg=C_NAVY,sz=10) ws12.row_dimensions[2].height=22 dashboard=[ ("Total patients enrolled", '=COUNTIF(\'1.DEMOGRAPHICS\'!D3:D22,"GT")', '=COUNTIF(\'1.DEMOGRAPHICS\'!D3:D22,"ST")', '=B3+C3', "Target: 60-80 total"), ("28-day mortality (PRIMARY OUTCOME)", '=COUNTIFS(\'10.OUTCOMES\'!C4:C23,"Dead",\'1.DEMOGRAPHICS\'!D3:D22,"GT")', '=COUNTIFS(\'10.OUTCOMES\'!C4:C23,"Dead",\'1.DEMOGRAPHICS\'!D3:D22,"ST")', '=B4+C4', "*** KEY OUTCOME ***"), ("28-day mortality rate (%)", '=IF(B3>0,ROUND(B4/B3*100,1),"—")', '=IF(C3>0,ROUND(C4/C3*100,1),"—")', '=IF(D3>0,ROUND(D4/D3*100,1),"—")', "Compare GT vs ST"), ("Bacteremia (positive blood culture) n", '=COUNTIFS(\'6.MICROBIOLOGY\'!H4:H43,"Positive",\'6.MICROBIOLOGY\'!C4:C43,"Blood-Peripheral")', "","","Divide by arm if needed"), ("MDR organisms n", '=COUNTIF(\'6.MICROBIOLOGY\'!R4:R43,"Yes")', "","","Key for Nepal AMR data"), ("Mean days to ANC recovery (GT arm)","=AVERAGEIFS('10.OUTCOMES'!E4:E23,'1.DEMOGRAPHICS'!D3:D22,\"GT\")","","","Secondary outcome"), ("Mean days to ANC recovery (ST arm)","","=AVERAGEIFS('10.OUTCOMES'!E4:E23,'1.DEMOGRAPHICS'!D3:D22,\"ST\")","",""), ("Mean days to defervescence (GT)","=AVERAGEIFS('10.OUTCOMES'!G4:G23,'1.DEMOGRAPHICS'!D3:D22,\"GT\")","","",""), ("Mean days to defervescence (ST)","","=AVERAGEIFS('10.OUTCOMES'!G4:G23,'1.DEMOGRAPHICS'!D3:D22,\"ST\")","",""), ("Mean hospital stay (GT arm days)","=AVERAGEIFS('10.OUTCOMES'!K4:K23,'1.DEMOGRAPHICS'!D3:D22,\"GT\")","","",""), ("Mean hospital stay (ST arm days)","","=AVERAGEIFS('10.OUTCOMES'!K4:K23,'1.DEMOGRAPHICS'!D3:D22,\"ST\")","",""), ("ICU admissions n","","","","From Treatment sheet"), ("True positive buffy coat smear n","=COUNTIF('8.BUFFY_COAT_DIAGNOSTIC'!K4:K23,\"True Positive\")","","","Diagnostic value"), ("True negative smear n","=COUNTIF('8.BUFFY_COAT_DIAGNOSTIC'!K4:K23,\"True Negative\")","","",""), ("Mean time saved vs culture (h)","=IFERROR(AVERAGE('8.BUFFY_COAT_DIAGNOSTIC'!L4:L23),\"—\")","","",""), ("Mean GT product cost (NPR)","=IFERROR(AVERAGE('10.OUTCOMES'!O4:O23),\"—\")","","","vs ~35000-40000 for apheresis"), ("Mean total episode cost (NPR)","=IFERROR(AVERAGEIFS('10.OUTCOMES'!N4:N23,'1.DEMOGRAPHICS'!D3:D22,\"GT\"),\"—\")", "=IFERROR(AVERAGEIFS('10.OUTCOMES'!N4:N23,'1.DEMOGRAPHICS'!D3:D22,\"ST\"),\"—\")","","Cost-effectiveness"), ("90-day survival (GT arm %)", '=IFERROR(ROUND(COUNTIFS(\'11.FOLLOW_UP\'!I4:I23,"Alive",\'1.DEMOGRAPHICS\'!D3:D22,"GT")/COUNTIF(\'1.DEMOGRAPHICS\'!D3:D22,"GT")*100,1),"—")', '=IFERROR(ROUND(COUNTIFS(\'11.FOLLOW_UP\'!I4:I23,"Alive",\'1.DEMOGRAPHICS\'!D3:D22,"ST")/COUNTIF(\'1.DEMOGRAPHICS\'!D3:D22,"ST")*100,1),"—")', "",""), ] for i,(label,gt,st,tot,note) in enumerate(dashboard): r=3+i ws12.cell(row=r,column=1,value=label) ws12.cell(row=r,column=1).font=fnt(bold=(i in [0,1,2]),sz=10,color=C_NAVY) ws12.cell(row=r,column=1).fill=fill(C_LBLUE if i%2==0 else C_WHITE) for c,v,bg in [(2,gt,C_LGREEN),(3,st,"FFF2CC"),(4,tot,C_CALC),(5,note,C_WHITE)]: ws12.cell(row=r,column=c,value=v) ws12.cell(row=r,column=c).fill=fill(bg) ws12.cell(row=r,column=c).font=fnt(sz=10,bold=(i in [1,2]),color=C_RED if i==1 else (C_GREEN if c==2 else "843C0C" if c==3 else C_NAVY)) ws12.cell(row=r,column=c).border=thin() ws12.cell(row=r,column=c).alignment=aln() ws12.cell(row=r,column=1).border=thin() ws12.row_dimensions[r].height=18 # ═══════════════════════════════════════════════ # SHEET 14 — CODEBOOK # ═══════════════════════════════════════════════ ws13 = wb.create_sheet("13.CODEBOOK") ws13.sheet_properties.tabColor = "808080" set_cols(ws13,[4,25,16,40,22,16]) hdr(ws13,1,1,"CODEBOOK — VARIABLE DEFINITIONS, NORMAL RANGES & CODING GUIDE",bg="595959",sz=12,mc=6,rh=28) for c,h in enumerate(["#","Variable","Data Type","Definition / Normal Range","Code Values","Sheet"],1): hdr(ws13,2,c,h,bg="595959",fg=C_WHITE,sz=10,rh=22) codebook=[ ("FN Definition","Clinical","Fever ≥38.3°C once OR ≥38°C >1h + ANC <500/mm³","As defined","3.FN_EPISODE"), ("ANC","Numeric /mm³","WBC × (Neutrophil%+Band%)/100 | Normal 1500-8000","<1000=neutropenia; <500=severe; <100=profound","4.LAB_CBC"), ("MASCC Score","Score 0-26","Multinational Assoc Supportive Care Cancer score","≥21=Low Risk; <21=HIGH RISK (hospitalize)","3.FN_EPISODE"), ("PCT (Procalcitonin)","Numeric ng/mL","Bacteremia marker (Shilpakar Nepal 2019)","<0.5=unlikely bact; 0.5-2=possible; >2=likely","5.LAB_BIOCHEM"), ("Galactomannan","Index","Aspergillus antigen","Index >0.5=positive; >1.0=strongly positive","5.LAB_BIOCHEM"), ("Beta-D-Glucan","Numeric pg/mL","Broad fungal marker (not Cryptococcus/Mucor)","<80=negative; >80=positive; >200=strongly positive","5.LAB_BIOCHEM"), ("ESBL","Categorical","Extended-Spectrum Beta-Lactamase","Positive/Negative/Not done","6.MICROBIOLOGY"), ("CRE","Categorical","Carbapenem-Resistant Enterobacteriaceae","Positive/Negative/Not done","6.MICROBIOLOGY"), ("MDR","Binary","Multi-Drug Resistant: resistant to ≥3 antibiotic classes","Yes/No","6.MICROBIOLOGY"), ("DTP","Minutes","Differential Time to Positivity (CLABSI indicator)","CVC positive ≥120 min before peripheral = CLABSI","6.MICROBIOLOGY"), ("GT Dose","mL/kg","Buffy coat granulocyte transfusion dose per infusion","Target 10 mL/kg per transfusion; ≥1×10¹⁰ cells","7.GT_TRANSFUSION"), ("TRALI","Clinical","Transfusion-Related Acute Lung Injury","New hypoxia + bilateral CXR infiltrates within 6h of transfusion","7.GT_TRANSFUSION"), ("Concordance","Auto","Buffy coat smear vs blood culture agreement","True Pos / True Neg / False Pos / False Neg","8.BUFFY_COAT"), ("28-day mortality","Binary","Death from any cause ≤28 days of FN onset","Alive / Dead — PRIMARY OUTCOME","10.OUTCOMES"), ("ANC Recovery","Days","Days from FN onset to ANC ≥500 for 2 consecutive days","Numeric — SECONDARY OUTCOME","10.OUTCOMES"), ("Defervescence","Days","Days from FN onset to afebrile >24h without antipyretics","Numeric — SECONDARY OUTCOME","10.OUTCOMES"), ("ELN 2022 Risk","Category","European LeukemiaNet AML risk stratification","Favorable/Intermediate/Adverse","2.MALIGNANCY"), ("ECOG PS","Score 0-4","Performance Status","0=Normal; 1=Ambulatory; 2=<50% bed; 3=>50% bed; 4=Bedbound","1.DEMOGRAPHICS"), ("HLH Screen","Panel","Hemophagocytic Lymphohistiocytosis","Ferritin>10000+Triglyc elevated+Fibrinogen low+D-dimer high","5.LAB_BIOCHEM"), ("Mucositis","WHO 0-4","WHO Mucositis Scale","0=None; 1=Soreness; 2=Erythema+ulcers; 3=Ulcers-liquid diet only; 4=No alimentation","3.FN_EPISODE"), ("Sepsis-3","Clinical","Sepsis=SOFA increase ≥2 + suspected infection","Septic Shock=vasopressor needed + lactate >2 mmol/L","3.FN_EPISODE"), ("BMI","Auto-calc","Body Mass Index — auto from height/weight","Normal 18.5-24.9; Underweight <18.5 (common in Nepal patients)","1.DEMOGRAPHICS"), ("Clinical Response D7","Category","Response at Day 7 of treatment","CR=Afebrile+ANC recovering; PR=one criterion; NR=neither; PD=worsening","10.OUTCOMES"), ("DM Degree Level","Context","This is a DM (Doctorate of Medicine) thesis — higher evidence standard required","RCT design; CONSORT reporting; CTRI registration","All sheets"), ("ASH Submission","Target","Blood Advances (IF 7.7) — Category: Phagocytes/Granulocytes/Myelopoiesis","Max 4500 words; 250-word abstract; numbered NLM refs; CONSORT diagram","N/A"), ] for i,(v,dt,defn,code,sh) in enumerate(codebook): r=3+i ws13.cell(row=r,column=1,value=i+1).font=fnt(sz=9) ws13.cell(row=r,column=2,value=v).font=fnt(bold=True,sz=9,color=C_NAVY) ws13.cell(row=r,column=3,value=dt).font=fnt(sz=9) ws13.cell(row=r,column=4,value=defn).font=fnt(sz=9) ws13.cell(row=r,column=4).alignment=aln(h="left",wrap=True) ws13.cell(row=r,column=5,value=code).font=fnt(sz=9,color=C_RED) ws13.cell(row=r,column=6,value=sh).font=fnt(sz=9,color=C_BLUE) bg = C_LBLUE if i%2==0 else C_WHITE for c in range(1,7): ws13.cell(row=r,column=c).fill=fill(bg) ws13.cell(row=r,column=c).border=thin() ws13.row_dimensions[r].height=18 # Save output="/home/daytona/fn-thesis/FN_HematMalig_DataEntry_CSH.xlsx" wb.save(output) print("SUCCESS:", output) PYEOF

ls -lh /home/daytona/fn-thesis/