In higgi13425/medicaldata: Data Package for Medical Datasets

knitr::opts_chunk$set(echo = TRUE)

Source: This data set is provided generously by Frank Harrell, from his website here, as the dataset "abm".

Description This dataset is a subset of the data from a Duke University study of acute meningitis, as provided by Frank Harrell. The patients were found to have clinical symptoms of meningitis, which include a painful, stiff neck with a limited range of motion, headache, light sensitivity, high fever, confusion, and lethargy. This can progress rapidly, and can prove fatal. Bacterial meningitis can be treated successfully with antibiotics, if given early. Antibiotics are unnecessary and unhelpful in viral meningitis, and can cause allergic reactions or other adverse events in some patients. Clinically, viral and bacterial meningitis have very similar symptoms, due to the common cause of inflammation of the meninges, the three membranous layers that protect the brain and spinal cord. A spinal tap (aka lumbar puncture, or LP) can be performed to obtain cerebrospinal fluid (CSF) for analysis to help classify cases as bacterial or viral in origin. Timely identification and early treatment of bacterial meningitis can be life-saving.

Potential Analyses

Some interesting potential analyses include classifying cases as abm or not abm with logistic regression or forms of machine learning. Deriving variables, including the csf to blood glucose ratio, and the months from peak summer (June/July in the Northern Hemisphere) may improve prediction.

Abstract

This data set contains 581 participants with symptoms of meningitis who were evaluated with blood tests and a spinal tap to obtain cerebrospinal fluid (CSF). The findings of the lab tests are presented as measures of blood and csf. These normally are in homeostasis, with similar levels of glucose and other small molecules. Bacterial infection tends to lower csf_glucose, as this is consumed by bacteria. Risk factors, including month (more abm in summer), sex, race, and age are included. Neutrophil (neut) and immature neutrophil (band) counts go up with bacterial infection, while lymphocyte (lymph) and monocyte (mono) counts tend to go up with viral infection. The gram stain (gram) detects bacteria, and is helpful when positive. Culture results (cult) for blood and csf can be helpful after the fact (generally take days, while we have to make a clinical decision about antibiotics immediately). The outcome variable for modeling is abm (0 if absent, 1 if acute bacterial meningitis is present).

Study Design

Observational Cohort

Subjects & Variables

A data frame with 581 observations of patients with symptoms of meningitis and 22 variables

Variables

casenum - case number, from 1 to 581; type: double

year - 2 digit year, from 68 (1968) to 80 (1980), 72 missing; type: double

month - month, from 1 (January) to 12 (December), 81 missing; type: double

age - age in years, 81 missing; type: double

race - coded as 1 = Black, 2 = White, 85 missing; type: double

sex - gender, coded as 0 = male and 1 = female, 81 missing; type: double

blood_wbc - white blood cell count in blood, in thousands of cells per cubic millimeter, 141 missing; type: double

blood_neut_pct - Percentage of white blood cells that are neutrophils, considered indicative of acute bacterial infection, in blood, 146 missing; type: double

blood_band_pct - Band cells, also known as immature neutrophils, considered indicative of acute bacterial infection, in blood, in percent of the total white blood cells, 153 missing; type: double

blood_gluc - Blood glucose, in milligrams per deciliter, 258 missing; type: double

csf_gluc - CSF (cerebrospinal fluid) glucose, in milligrams per deciliter, 129 missing; type: double

csf_prot - CSF (cerebrospinal fluid) protein, in milligrams per deciliter, 249 missing; type: double

csf_rbc - CSF (cerebrospinal fluid) red blood cells, thousands of cells per cubic millimeter, 271 missing; type: double

csf_wbc - CSF (cerebrospinal fluid) white blood cells, thousands of cells per cubic millimeter, 101 missing; type: double

csf_neut_pct - CSF (cerebrospinal fluid) neutrophil percentage, percent of total white blood cells in CSF, 132 missing; type: double

csf_mono_pct - CSF (cerebrospinal fluid) monocyte percentage, percent of total white blood cells in CSF, 165 missing; type: double

csf_lymph_pct - CSF (cerebrospinal fluid) lymphocyte percentage, percent of total white blood cells in CSF, 162 missing; type: double

gram - gram stain result, values 0-6, 313 missing; type: double

csf_cult - result of csf culture for bacterial growth, values 0-6, 307 missing; type: double

blood_cult - result of blood culture for bacterial growth, values 0-6, 434 missing, 11; type: double

subset - subset, training = 1 or test = 2; type: double

abm - the outcome variable, acute bacterial meningitis, 0 = absent or 1 = present, 80 missing; type: double

Details

Bacterial meningitis occurs in 1 in 100,000 people per year in the United States, most commonly in people between 16 and 23 years old, with additional age peaks in infants and young children, and the elderly. Early symptoms include headache, fever, and pinprick rash of reddish-purple tiny spots. The peak season for bacterial meningitis is in dry winter months in each hemisphere (December-February in the Northern Hemisphere). Bacterial meningitis has a fatality rate of 15-20%, which is higher in the elderly. Untreated bacterial meningitis due to Streptococcus pneumoniae or H. influenzae approaches 100% mortality.

Viral meningitis generally resolves with supportive care, but bacterial meningitis requires early use of antibiotic therapy. A subset of patients will require a head CT (computed tomography) scan before a lumbar puncture to obtain CSF, which must occur before antibiotics are given. The CSF (cerebrospinal fluid) is sent to the lab for cell count and differential, glucose, protein, gram stain, and culture. Normally, the meninges are part of the blood-brain barrier, which keeps assorted toxins we ingest out of the brain. Proteins and large molecules from the bloodstream are not able to reach the CSF normally, and even smaller molecules like glucose equilibrate slowly, so that CSF glucose lags behind changes in blood glucose. Normal CSF has some white blood cells, with around 70% lymphocytes and 30% monocytes, with very few neutrophils. When bacteria begin to multiply in the CSF, CSF protein levels go up, glucose is consumed, and white blood cells (largely neutrophils) arrive to fight the bacteria. Viral infections tend to attract more lymphocytes and monocytes. Characteristic findings in bacterial meningitis include low CSF glucose, a low CSF to serum glucose ratio, high CSF protein, and a high CSF white blood cell count, usually composed of neutrophils. However, the spectrum of CSF values in bacterial meningitis is so wide that any one of these findings is of little value. About 20% of lumbar punctures draw a bit of blood, which is seen when there are more than 100,000 RBCs per cubic mm. This blood will also increase the CSF WBCs by one WBC per every 500-1000 RBCs, and may require adjustment of the WBC number.

Empiric treatment with antibiotics is begun as soon as the CSF reaches the lab, often with a combination of ceftriaxone plus vancomycin, and ampicillin is added in the elderly to cover Listeria. Meropenem is often used in the immunocompromised for broader coverage including Listeria and Pseudomonas. The gram stain helps detect bacteria in the CSF, but is only \~60% sensitive, and will usually miss tuberculosis, toxoplasmosis, and fungal meningitis. CSF culture (growing the bacteria) is more sensitive, but takes several days.

The primary analysis task is to classify non-bacterial (usually viral) (abm = 0) vs. bacterial (abm = 1) cases, as published in Spanos A, Harrell FE, Durack DT (1989): Differential diagnosis of acute meningitis: An analysis of the predictive value of initial observations. JAMA 262: 2700-2707. There are data on 581 patients, with typical levels of missing data in clincial observational studies done in the days of paper charts, so you may choose to impute some of the missing data. Some of the variables in the published paper need to be derived, including the CSF to blood glucose ratio, and the number of months from peak of summer (in North Carolina, in the Northern Hemisphere). In addition to imputation, modern machine learning classification techniques can be applied and compared to logistic regression results.

Source This data set is provided generously by Frank Harrell, from his website here, as the dataset "abm".

Citation(s)

These data were published as Spanos A, Harrell FE, Durack DT (1989): Differential diagnosis of acute meningitis: An analysis of the predictive value of initial observations. JAMA 262: 2700-2707, which can be found here.

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