🧭 1. DEPTh Typing: This is a Diagnostic Challenge So your challenge = “Given a biological isolate (bio sample), how do we determine what organism it is — using a database comparison with a score and a hit?” ➡ DEPTh type: Diagnostic   The object of study = diagnostic accuracy  of a computational or laboratory index test Index test:  sequence or spectrum matching algorithm Reference standard:  species identification (e.g., culture, gold-standard sequencing) 🔬 2. Diagnostic Lo

Abstract Choosing whether to treat predictors as continuous or categorical is one of the most recurrent—and most misapplied—decisions in clinical prediction model (CPM) development. Although categorization improves interpretability, it often sacrifices statistical power, calibration, and discrimination. This article integrates statistical evidence and clinical reasoning to define when, why, and how continuous variables should be modeled or categorized. A structured, evidence-

🧠 Overview Acute laryngitis  is the most common cause of hoarseness (dysphonia) .It is usually viral , self-limited, and involves inflammation of the laryngeal mucosa and vocal cords . When hoarseness occurs without other major airway symptoms , it is called “pure hoarseness”  — meaning the patient has voice change without dyspnea, stridor, dysphagia, or systemic toxicity . 🧩 Pathophysiology Normally, the vocal cords vibrate symmetrically to produce sound.In laryngitis: Vi

Introduction Why Use Cohen’s Kappa in Diagnostic Research? Cohen’s Kappa (κ)  is a widely used statistical measure for assessing agreement  between two raters or measurement methods that classify items into categorical outcomes. It adjusts for the agreement that could occur  by chance , providing a more realistic and conservative estimate of concordance. Purpose and Applications Measuring Inter-rater or Inter-method Agreement Kappa is primarily used to quantify the level of a

🔍 Background In the development of Clinical Prediction Models (CPMs) —tools that estimate a patient's risk of future events based on clinical features—researchers often report strong model performance when evaluated using the development dataset. However, these metrics can be misleadingly optimistic. This gap between perceived and true predictive ability is known as optimism . 📊 What Is Optimism? Optimism  in CPMs refers to the inflation of performance metrics (e.g., AUROC,

Machine learning isn’t a new species of science — it’s an evolution of the statistical logic that epidemiologists already use. We’ve always modeled the relationship between exposure and outcome, adjusting for confounders and exploring patterns. What ML brings is automation, scalability, and the ability to capture complex, nonlinear, interactive relationships that traditional regression often misses. 1️⃣ Level 1 — Traditional Regression: The Clinical Baseline Before diving int

🟡 START You begin by asking: What kind of problem am I trying to solve in my study? Common scenarios in clinical epidemiology : Identifying patients with a disease → diagnosis Predicting future outcomes → prognosis Estimating biomarkers or lab values → continuous prediction Finding hidden patient subgroups → phenotyping Simplifying many variables into a few patterns → data reduction 🔹 1. Do you have labeled data? YES →  Go to Supervised Learning  (you know the outcome) e.g.

1️⃣. Definition and Pathophysiology Hyperthyroidism  = overproduction of thyroid hormones ( T3, T4 ) by the thyroid gland → suppressed TSH . Thyrotoxicosis  = clinical syndrome of excess circulating thyroid hormone, regardless of cause (e.g., Graves, thyroiditis, toxic nodular goiter). Pathophysiology summary: ↑ T3/T4 → ↑ basal metabolic rate ↑ β-adrenergic receptor sensitivity → palpitations, tremor Feedback inhibition → ↓ TSH from pituitary 2️⃣. Common Causes Category Disea

🎯 1. Goal of Therapy Normalize Free T4 (FT4)  and Free T3 (FT3)  levels. TSH  is not reliable early — it remains suppressed for weeks to months  even after hormones normalize. The primary lab for dose adjustment = FT4 (± FT3) . 🧪 2. Monitoring Schedule Time after starting MMI Lab to Check Why Baseline TSH, FT4, FT3, CBC, LFT Starting point & safety 4–6 weeks after starting FT4 ± FT3 (ignore TSH) Adjust dose Every 4–6 weeks thereafter FT4 ± FT3 Continue titration Once euthyr

“N in research represents the p-value — it reflects how believable a result is, or whether the difference is simply due to random change.” In clinical research, we often treat N , the sample size, as a mechanical requirement — something to “get enough patients” or “reach significance.”But that view is incomplete. N is not just a number; it is a claim about credibility. It defines how convincingly we can argue that a difference is real , not random . It connects p-values , cl

Introduction Removing duplicate citations is a vital step in systematic reviews. Duplicate records not only inflate the screening workload but also introduce potential bias if counted more than once in the analysis. Effective deduplication ensures that each unique study is represented only once, maintaining both accuracy  and efficiency  in the review process. One widely validated and reproducible approach is the multi-step deduplication strategy  in EndNote, often referred t

Abstract Logistic regression and neural networks share a deep mathematical and conceptual structure. Both compute weighted sums of...

Clinicians often juggle questions that look  similar but actually demand different scientific logics. The DEPTh model (Diagnosis,...

Concept → How it works → Stata commands → How to find the inputs 1) Concept—what pmsampsize is (and why we use it) pmsampsize is a...

For many years, the 10 Events-per-Variable (EPV)  rule was the default checkpoint for building clinical prediction models. The idea is...

1️⃣ What Is the Fontan Procedure? The Fontan procedure  is a palliative cardiac surgery  performed for children with single-ventricle congenital heart defects , where only one ventricle is capable of supporting systemic circulation. ➤ Purpose: To separate systemic and pulmonary circulation  in patients who cannot undergo a biventricular repair. ➤ Indications: Common congenital heart diseases requiring Fontan include: Tricuspid atresia Hypoplastic left heart syndrome (HLHS) Do

🔹 Definition Orchitis  is an inflammation of the testicular parenchyma .It can occur as: Primary orchitis  (rare, often...

🔹 Definition Epididymitis is the inflammation of the epididymis , the coiled duct located posterior to the testis responsible for sperm...

Introduction The Receiver Operating Characteristic (ROC)  curve is a cornerstone metric in both diagnostic and prognostic model...

Category Drug Dose & Route Frequency Duration Notes Topical steroid (first-line) Hydrocortisone 1% cream Thin layer over lesion bid 5–7...

Antifungal Regimens for Onychomycosis Drug Fingernails Toenails Notes Terbinafine 250 mg PO once daily × 6 weeks 250 mg PO once daily ×...

Literature Review – No strict system; risk of bias – It is informal, narrative, and selective – Purpose: to show what’s known, critique,...

Diagnosis (Lesion Characteristics) 🟢 Tinea corporis (ringworm of body) Annular (“ring-shaped”) lesion  with erythematous, scaly, raised...