Basic Conventions 1

Basic Conventions1

In a binary 0 or 1, 0 implies absence of the named event and 1 implies its occurrence, e.g., a diagnosis, a positive lab test, taking a medication, etc.Age is in years unless otherwise indicatedPt: patient; ptid: patient identification numberDX: diagnosisTX: treatmentRT or XRT: radiation therapy Ca: cancer, as CaP: cancer of the prostateHIV: human immunovirusAIDS: acquired immune deficiency syndromeSTD: sexually transmitted diseaseHSV2: herpes simplex virus 2; genital herpes.

Basic Conventions2

CD4: Cell count of a type of T-cell that helps oppose HIV. The higher the count, the healthier is the patient.

VL: Viral load; plasma level of viral RNA; a measure of severity of viral disease. Log(VL) is usually used because of strong right skew.

Alt, ast: alanine, aspartate aminotransferase; measures liver health.Cholesterol, triglycerides: measures heart health.

DB16. HSV2 in HIV Patients-1

• Background: HIV patients often have comorbidities, one of which is the STD HSV2.

• Q: Do people with/without HSV2 have different CD4 counts and/or viral load (VL)? (Stratify by HIV meds, which artificially lowers VL and raise CD4.)

DB16. Data Definitions

HSV2: 1=infected, 0=not. Sex: 1=m, 0=f. Yrshiv: no. of years pt has had HIV. Age: years. Race: 1=EuroAmer, 2=AfroAmer, 3=HispAmer, 4=other. Cd4: CD4 count. Vl1,vl2, vl3: 3 viral load assays. Control: 1=detectable VL, 0=not. Acyclovir: 1=on med for HSV2, 0=not. Hivmeds: 1=on med for HIV, 0=not. Sample of data format:

id hsv2 sex yrshiv age race cd4 vl1 vl2 vl3 control acyclovir hivmeds156 0 1 2 30 2 235 75000 14331 75000 0 0 0413 0 1 9 42 4 709 0 0 0 1 0 1

DB17. Prostate Cancer in HIV Patients-1

• Background: HIV patients who acquire prostate cancer (CaP) may follow a different disease pattern than non-HIV patients.

• Q: What characteristics are different in HIV patients with and without CaP?

• Q: What variables predict CaP in HIV patients?

DB17. Data DefinitionsEthn: 1=EuroAmer, 2=AfroAmer, 3=Hisp Amer, 4=other. Hivyrs: years since HIV dx. %cd4: %CD4 cells of all T cells. Lowcd4: CD4 nadir. Haart: On HAART treatment or not. Dxcap: Prostate cancer diagnosed or not. Dre: Digital rectal exam positive or not. On-testost: Being treated with testosterone or not. (Testosterone increases risk of CaP.) Sample of data format:

Age ethn hivyrs cd4 %cd4 vl lowcd4 haart dxcap psa dre on-testost 36 1 9 954 26 52556 310 0 0 0.4 0 0 41 3 10 710 56 75000 538 0 0 0.7 1 0

DB18. Group A Strep Pneumonia Outbreak

• Background: A sudden outbreak of Group A Streptoccum pneumoniae occurred at the Marine Corps Recruit Depot in San Diego, serious enough to have had special coverage by CNN.

• Q: Did the Grp A strep pneumonia evince any unique characteristics, i.e., different from other pneumonias?


Grpa: Group A Strep=1, other pneumonias=0.

Multilobe: x-ray shows more than one lung lobe infected=1, single lobe=0.

Dayshosp: no. of days spent in hospital.

Remaining variables (lab test results, vital signs, and symptoms) are obvious.

DB19. AIDS Mortality

• Background: Of a sample of 1224 AIDS patients who died, time to death varied with several influencing effects and potential co-causes of death.

• Q: What variables affect the survival time• of AIDS patients? How do they affect it?

• Q: Can survival time be predicted by certain variables? If so, which?


Serodate: Date of test showing pre-infection exists.Cod: Cause of death. 1, 2: primary, secondary.Pcp: pneumocystis carinii pneumonia.Oi: Opportunistic infection.Cmv: Cytomegalovirus.Mac: Mycobacterium avium complex.Cd4_200: CD4<200.Waltreed_staging: staging (severity) of infection used at Walter Reed Army Medical Center.Gangacyclovir, fluconazole, septra, pentamidine, azithro, dapsone: types of antibiotic medicine.

Hepbc, hepbs: hepatitis B core, surface antigen type.

Hepc: hepatitis C.

DB20. Erectile Dysfunction in HIV Patients

• Background: Erectile dysfunction (ED) in otherwise healthy adults has received considerable attention, but little is known about its pattern in HIV patients.

• Q: What is its rate of occurrence?

• Q: What HIV characteristics are different between patients with and without ED?


Ed_or_not: 1: has ED; 0: does not have ED.

Lowest cd4, current cd4: CD4 counts.

Current vl, highest vl: Viral Load counts.

Yrs_of_hiv: Years patient has had HIV.

Age: Patient’s years of age.

Haart_1: Pt has had HAART treatment: 1; has not had HAART treatment: 0

DB21. HIV Patients with Syphilis

• Background: Co-morbidities are a serious problem with HIV patients. Syphilis is a severe one, but little is known about its effect on the health of these patients.

• Q: What health characteristics of HIV patients change upon contracting syphilis?


• Race: 0=EuroAmer, 1=AfrAmer, 2=HispAmer, 3=AsianAmer.

• Before: before contracting syphilis.• After: after contracting.• Hepbc, hepbs: hepatitis B, core and surface

antigen type, respectively.• Hepc: hepatitis C.• Hsv: herpes simplex virus 2 (genital).• Everonhaart: has been treated with HAART

med cocktail.

DB22. Pediatric Snake Bites

• Background: Rattlesnake bite data from San Diego Poison Center on 204 children

• Q: Is location of bite affected by age, sex, and/or season?


• Age: years. Sex: male = 1, female = 2.• Agegroup: 2 = 13 (toddler), 7 = 49 (child),

11 = 1012 (tween), 15 = 1318 (teen).• Location: 2/3 = hand/arm, 4 = face,

5/6 = leg/foot, 7 = unknown. • Locbinary: 2 = hand/arm, 5 = leg/foot.• Month of Bite: 1 = Jan, 2 = Feb, etc. • Season: 1 = winter (months 1, 2, 3),

2 = spring (months 4, 5, 6), etc.

DB23. Adult Snake Bites

• Background: Rattlesnake bite data from San Diego Poison Center on 625 adults

• Q: Is location of bite affected by age, sex, and/or season?

• Q: Are adult findings different from those for children (DB22)?


• Age: years. Sex: male = 1, female = 2.• Agetrinary: 25 = <35, 45 = 35-55, 65 = >55.• Location: 2/3 = hand/arm, 4 = face,

5/6 = leg/foot, 7 = unknown. • Locbinary: 2 = hand/arm, 5 = leg/foot.• Month: 1 = Jan, 2 = Feb, etc. • Season: 1 = winter (Jan/Feb/Mar), 2 = spring

(Apr/May/Jun), etc.

DB24. Weight Estimation in the ER

• Background: Many drug dose levels depend on the patient’s weight. In the ER, patients are not always lucid. This DB has true measures, various estimates, and various covariates that could be used in an estimation equation.

• Q: What is the best way to estimate a patient’s weight? Is this estimate reliable?


• Age: years. Sex: 1 = female, 2 = male.• Ht: height (cm). Wt: weight (kg). • Est: estimate.• Nok: next of kin. Phys: physician. • Inv: investigator. • Circ: circumference. Abd: abdomen.• 1 & 2: repeated readings by 2 physicians.• Tibia length: standardized length of tibia.

DB25. Snoring as a Sleep Problem

• Background: Snoring is thought of as an adjunct to sleep problems, not a cause. Accepted causes are apnea, hypopnea, obesity, age, et al.

• Q: Do our data show that snoring is a cause of sleep problems?

• Q: What other causes do the data show?

DB25. Data Definitions• Epworth: sleepiness scale. ESS & FOSQ: range 024• Fosqtotal: Functional Outcome of Snoring Quotient• Age: years. Sex: 1 = female, 2 = male• Bmi: body mass index = 703*weight (lb)/height2 (in)• Ahi: apnea-hypopnea index—episodes per hour av• Dur: duration (hrs) of snoring > 50 dB• Max: maximum dB level of snoring• Avdb: mean dB level of snoring when > 50 dB• Percent: % of sleep time when mean dB > 50• Snoring, obesity,…, stroke: in pt’s record (1)• …byspouse: bed partner complains

DB26. Vulvar Cancer Survival

• Background: DB has 45 vulvar cancer patients with numerous putative correlates, e.g., age, overweight, tobacco use, immunocompromise, diabetes,….

• Q: What variables relate to cancer stage?

• Q: What variables relate to number of positive lymph nodes?

• Q: What variables predict survival?

DB26. Data Definitions1• Stage: Of Ca. 15 respectively: stage 1a, 1b, 2, 3, 4.• Nodes: Affected (1) or not (0). Dead: yes (1) or no (0).• Years: Diagnosis to death if dead or last f-u if not.• Gravididity: # pregnancies. Parity: # births.• BMI: body mass index = 703xlbs/in2.• Tobacco: 1 = current, 2 = quit, 3 = never.• Warts: No. of warts.• Degreevin: Severity of VIN infection on 15 scale.• Sxlength: Duration (years) of symptoms.• Los: Length of surgery (hours).• Ebl: Estimated blood loss (ml) during surgery.

DB26. Data Definitions2• Histology: Squamous cells (1) or non-squamous (2).• Nodestotal: Number of affected lymph nodes.• Present (1) or absent (0) conditions:

• Hpv (human papillomavirus), • condyloma (wart-like growth on vulva), • vin (a related virus), • dm (diabetes), • steroids (using or not), • imcomp (immunosupressed), • margins (Ca spread outside locality), • xrt (radiotherapy or not), • chemo (chemotherapy or not).

DB27. Artificial Hip Placement• Background: Artificial hips must be

carefully positioned to be effective. Operated and non-operated leg lengths and hip angles are compared for 69 patients, 38 with x-ray guidance and 31 without, all read twice for reliability.

• Q: Does x-ray during placement increase accuracy?

• Q: Are the readings reliable between and within readers?


• Obsrvr. Reader 1 or 2• X-ray. 1: x-ray used, 0: not used• Pre, preop, postop. Pre- or post-operative• Op, non. Operated or non-operated hip• 1, 2, av. 1st, 2nd, mean rdg. by same reader• Lld. Leg length difference between readings• Abdang. Abduction angle (from vertical)• Distances in centimeters, angles in degrees

DB28. Does Handling Worsen Injuries

• Background: Badly injured (wounded) patients trucked or airlifted to hospital are roughly handled and become cold. Ten pigs are injured, cooled, and roughly handled, and their conditions measured.

• Q: What is the effect of cooling and/or handling? When it is severe enough to risk death?


The pigs are cooled progressively until their core temperatures reach prescribed levels, then are jostled and dropped from a few-inch height. Heart rate (HR), mean arterial pressure (MAP), pH, and CO2 are measured initially and at each level, along with incremental number of minutes to reach that level. Levels were 38º, 35º, 32º, 29º, 26º, 23º, and 20º. Death or not is recorded, with final temperature.

DB29. Compare OR Thermometer Types

• Background: In the OR, different types of temperature measurement used were (1) esophageal, (2) tympanic, and temporal arterial scanner (TAS) on (3) forehead and (4) forehead plus behind ear.

• Q: Do they measure the same? If not, can one be made equivalent to another by a linear transform?

• Q: Is each internally consistent?


Five temperature measurements (temp) are made 10 minutes apart on each of 48 patients by four types of thermometer:

eso: esophageal

tym: tympanic

for: TAS on forehead

ear: TAS on forehead + ear

Example. fortemp2: the 2nd reading of the TAS on the forehead

DB30. Laryngectomy Survival

• Background: Three modes of therapy for larynx cancer are radiation therapy (RT), larynx conservation surgery (CS), or a combination. When therapy fails, a salvage total laryngectomy (STL) may be tried.

• Q: What is survival rate through time?

• Q: Does survival after laryngectomy vary with type of initial therapy?


Retrospective study, giving survival outcomes of STL (died: 1 = died, 0 = not) and years to death or last follow up

for Grp 1: 53 initial RT failures Grp 2: 6 initial CS failures Grp 3: 5 initial RT+CS failures

DB31. Positioning Patients in H&N RT

• Background: Patients are held in a helmet-mask for repeated H&N (head & neck) RT to localize RT focus on the tumor and avoid adjacent tissue. Independent exact measurement of position’s deviation from 0.

• Q: Is the RT focus accurate on average? • Q: Does the RT focus change in a patient

over repeated treatments? If so, in what dimensions?

• Q: Does therapist or machine affect accuracy?


• 13 pts with 20-30 treatments each: 320 obs.• Sessnr: session number. Nrtx: no. treatmts.• x, y, z: position in 3 respective dimensions.• Octant: position of error in 1 of 8 directions.• Therapist: ID of person administering RT.• Machine: ID of radiation machine used.• Firstlast: marks 1st, last session per patient.• Wtdif: Weight loss (lbs) during therapy.• Sex: 1 = m. Age: years. • Dose: amount of radiation.

DB32. Anesthetic Type v. Recovery Time

• Background: There is a variety of anesthetics, which vary with dosage, with type of procedure, and with patient characteristics.

• Q: Does anesthetic type influence time to start procedure, length of procedure, and/or time to recovery? Do dose, age, and/or weight affect these variables?


• Anestype: primary anesthetic type (some have others added, not dominating effect). 1: ketamine IV, 2: ketamine IM, 3: a narcotic (versed, fentanyl, morphine), 4: propofol.

• Dose: standardized dose, i.e., scaled to same level of intended anesthesia.

• Age: years.• Wt: weight kg. (Most adults defaulted to 70.)• Procedure time, recovery time, discharge

(dc) times in minutes.

DB33. Reliability in Reading X-Rays

• Background: Interpretation of an x-ray may profoundly affect a patient.

• Q: Does a radiologist read the same result consistently?

• Q: Do different radiologists read the same result?

• Q: How important are training and experience in reading x-rays?


• Three radiologists (G, C, and S) judge disease severity shown in radiographs from 100 cancer patients.

• Each reads each x-ray 3 times: once, wait a month, shuffle order, reread, wait a month, shuffle order, read a third time.

• Each reading is a judgment of cancer stage, i.e., how far cancer has progressed, on a 0 to 5 scale.

DB34. Disruptive Back Pain in Pilots

• Background: Helicopter pilots suffer a disproportionate amount of back pain which affects their safety and efficiency.

• Q: What factors are associated with pilot back pain? (Type of aircraft? Length of flight? Frequency of duty? Height? Obesity? Use of medications? Presence of neurologic symptoms? Etc.)


• Presence (1) or absence(0):

Presence of back pain, affects flight, seen by physician, taking medications, neurologic symptoms.

• Age (years), height (in.), weight (lbs.).• Type of aircraft: 1 = AH-1W, 2 = UH-1N.• Days per week: days of flight per week

regularly scheduled.

DB35. Effect of Fasting on Cholesterol Measurement

• Background: Conventional wisdom says that cholesterol measurement is not reliable unless taken after fasting.

• Q: Are fasting and non-fasting cholesterol readings different?

• Q: Are they internally consistent?

• Q: Can fasting cholesterol be estimated from non-fasting cholesterol?


• Sex1f: Female (1), male (2). Age: years.• Suffix fast implies measurement taken after

fasting, eat implies without fasting.• Tot: Total cholesterol.• Ldl: Low density lipoprotein level.• Hdl: High density lipoprotein level.• Tg: Triglyceride level.• Glu: Glucose level.

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Basic Conventions 1