What is categorical data?
- Data that fits into categories.
- It can be nominal (no order implied): Race: Black, White, other
- or ordered: income: < $20k, $20k-$80k, > $80k.
How do you calculate variance and standard deviation?
- Where x bar = average, n = sample size, x2 = sample, and S2 = variance.
- The standard deviation, S, is the square root of the variance.
What is a normal distribution?
aka Gaussian distribution, it is simply a symmetrical bell shaped distribution where the mean, median, and mode are all the same number.
What is the standard normal distribution?
- A normal distribution with a mean of 0 and a standard deviation of 1. 68% of data are within one standard deviation, 95% are within 2 standard deviations, and 99.7% are within 3.
How can we appraise the normal distribution of a graph?
- A histogram compares the distribution with a standard deviation curve so you can see how much they deviate from one another.
- A Q-Q plot compares the individual samples to the average, denoted as a diagonal line (the average) and dots (the individual samples)
- A Shapiro-Wilk test is a quantifiable test with the null hypothesis: the data are normally distributed. If p < 0.05, the data are NOT normally distributed.
What is the p-value?
The probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true.
How is this image skewed?
The image is left skewed because there are outliers on the left.
What is the difference between screening tests and diagnostics tests?
- Screening involves classifying asymptomatic people as likely or unlikely to have a disease or condition. (ie, identifies high risk individuals from a healthy population)
- Diagnostic tests are used to test individuals who are believed to be sick.
Compare primary prevention, secondary prevention, and tertiary prevention.
- Primary prevention: preventing a disease from occurring
- Secondary prevention: Preventing symptoms after a disease has its biological onset.
- Tertiary prevention: Treating symptoms to prevent death or other problems
Compare validity and reliability
- Validity: Asks if the test is measuring what it is supposed to. Are the results correct?
- Reliability: Do we get the same result over and over?
- A test can be reliable but not valid (consistently gives the wrong results, etc)
Compare internal validity and external validity.
- Internal validity: Does your test measure what it is supposed to measure?
- External validity: How well does the test generalize to the population at large?
How do you calculate sensitivity
- Sensitivity = true positives / (true positives + false negatives)
- = TP / (TP + FN)
How do you calculate specificity?
- Specificity = true negatives / (true negatives + false negatives)
- = TN / (TN + FN)
What is the criterion of positivity?
- The test value at which we assume a positive result for a test with a scale of result values. Ie, the cut off point.
- The criterion of positivity affects sensitivity and specificity.
When to optimize tests for specificity or sensitivity.
- For fatal diseases with no treatment, you want to optimize specificity so that you don’t give someone false bad news (ie, that they have HIV when they don’t).
- For treatable diseases, we want to optimize the test for sensitivity so that we can catch and treat the diseases.
How do you calculate accuracy?
Accuracy = (TP + TN)/ (TP + TN + FP + FN)
How do you calculate the positive predictive value?
- Positive predictive value = TP / (TP + FP)
- This reflects the probability that a positive test reflects the underlying condition being tested for.
How do you calculate the negative predictive value?
- Negative predictive value: TN / (TN + FN)
- A high NPV means that the test only rarely misclassifies a sick person as being healthy
What is a nucleoside and what is a nucleotide?
- Nucleoside: Nitrogenous base + sugar (eg, deoxyribose).
- Nucleotide: Nitrogenous base + sugar + phosphate.
Differentiate between DNA and RNA
- DNA has Deoxyribose, so the 2nd carbon (the first is the anomeric carbon) has an H instead of OH.
- DNA is double stranded, providing a longer half life, RNA is single stranded with a shorter half life.
- DNA: A-T, C-G. RNA: A-U, C-G.
- Ribonucleotides can also function as second messengers (cAMP, cGMP), energy donors (ATP, GTP), and carriers of electrons for oxidation-reduction reactions (eg, Nicotinamide adenine dinucleotide, aka NAD+))
What is the molecular structure of purines?
What is the molecular structure of pyrimidines?
What types of bonds are involved in DNA helices?
- Phosphodiester bonds form between neighboring 3’ and 5’ hydroxyl groups to form the DNA backbone.
- Hydrogen bonds between nitrogenous bases (A-T has 2 H bonds, C-G has 3 H bonds) keep the strands together.
- Van der Waals forces stabilize the double helix structure.
Describe the pathway to nucleotide synthesis
Describe the pathway through which nucleotides are synthesized from intermediates in the degradative pathway for nucleotides (ie, nucleotide salvage).