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PRACTICAL SESSIONS:
EPIDEMIOLOGY & STATISTICS
Scenario
An outbreak of gastroenteritis occurred in Bandar Tun Razak, a suburban
neighborhood, on the evening of April 28. A total of 89 people went to the
emergency departments of the three local hospitals during that evening. No more
cases were reported afterward.
The patients complained of headache, fever, nausea, vomiting and diarrhea. The
disease was severe enough in 19 patients to require hospitalization for
rehydration.
The local health department was immediately notified of a potential food-borne
outbreak of gastroenteritis in Bandar Tun Razak.
Exercise 1
1. Define epidemic, endemic and pandemic.
2. Describe the gastroenteritis outbreak according to disease transmission and
epidemiological triad.
3. What are the possible causes of the outbreak?
4. List and discuss steps that should be taken in outbreak investigations
5. What further information needed?
Exercise 2
The epidemic team, including a medical epidemiologist (public health physician
Health Officer), health inspectors and a nurse, visited the local hospitals to
interview the attending physicians, the patients and some of their relatives. Some
stool samples were obtained from patients for microbiologic identification of the
causative agent.
The distribution of the disease by person (age and gender) was found as follows:
Age group
0 - 5 yr
6 - 10 yr
11 yr and
older
Total by
gender
Please calculate the totals for each column and row and their corresponding
percentages to try to determine if there are any important differences by age or
by gender. Interpret your findings.
Exercise 3
Therefore the epidemic team investigated the places where affected persons,
their relatives and neighbors ate that day (April 28). The following table shows
the team's findings:
Place
People
who
attended
Ill
people
Attack
rate
People
who did
not
attend
Ill
people
Cafeteria
LRT
207
61
157
47
Kedai
Makan Ali
246
25
122
13
Restaurant
ABC
475
68
189
29
Elementary
school
cafeteria
239
67
495
22
Attack
rate
Relative
risk
Please calculate the attack rates per 100 (incidence rates per 100) by place to try
to determine where the contaminated meal was served. For each place compare
attack rates (AR) for those who attended with attack rates for those who did not,
by using the relative risk (i.e., RR = AR in attendees/AR in non attendees).
Interpret your findings.
Exercise 4
Once the implicated place was determined, the investigation centered on the
food. The following table includes the food items served in that place on April 28:
Food
Item
Beef
rendang
Burger
Salad
276
218
105
28
21
49
266
131
297
27
14
15
Baked
potato
139
11
213
31
88
48
279
25
175
18
203
49
Fruit
cocktail
Ice
cream
Relative
risk
Important note: None of the kitchen personnel were ill. The names of the kitchen
personnel and their participation in the food preparation are as follows: Ms Mary
prepared the beef rendang and the potatoes, Johan prepared the salad and the
fruit, Salmah served all dishes except the ice cream, and Jamilah prepared the
burgers and served the ice cream. The ice cream was a commercial brand and
was bought at a nearby supermarket.
Please calculate the attack rates per 100 (incidence rates per 100) by food item
to try to determine the one that was probably contaminated. Compare attack
rates (AR) for those who ate the food item with attack rates for those who did not
eat the food item, by using the relative risk (i.e., RR = AR in those who ate the
food/AR in those who did not eat the food).
Interpret your findings.
Exercise 5
Given that the epidemic team worked fast enough and the implicated meal(s)
was (were) identified before all food leftovers were discarded, food samples from
some meal leftovers were taken to the laboratory. In addition, stool samples were
taken from the kitchen personnel who prepared or handled each different food
item.
The laboratory confirmed that Salmonella toxin was present in some of the food
samples and that one of the kitchen personnel of that place had the same
Salmonella species. Furthermore, the Salmonella species found in the food and
the kitchen worker was the same species found in stool samples of the patients.
Please discuss these findings and identify the kitchen worker possibly
responsible for the outbreak.
Discuss the general principle of prevention and control of gastroenteritis outbreak.
Screening: Definition
Screening Test
Screening program:
Requirements (I)
Screening vs Diagnosis
z In
Screening program:
Requirements (II)
Signs present to indicate disease presence
Screening test acceptable and harmless
z Screening test must be valid
z Yield of screening must be high
z Diagnostic work-up for a positive test must
have acceptable morbidity
z Screening exercise must be cost-effective
z
Dichotomous
z
+ve or -ve
Continuous
z
Positive
A
True-positive
B
False-positive
Negative
C
False-negative
D
True-negative
Sensitivity =
Sensitivity
Sensitivity is the
proportion of those
with the disease who
tested positive
Indicates how good a
test is at identifying
the diseased
Specificity
z
Specificity is the
proportion of those
without the disease
who tested negative
Indicates how good a
test is at identifying
the non-diseased
No disease
TEST RESULT
Presence or absence
determined by a
gold standard
Categorical
Validity
Sensitivity and specificity
The disease as
outcome variable
A
A + C
x 100
Specificity =
D
B + D
x 100
Predictive values
TRUTH
z Assess
Disease
Positive
A
True-positive
B
False-positive
Negative
C
False-negative
D
True-negative
PV+ =
Predictive values
PV of a positive test is the
proportion of individuals
who test +ve and have the
disease
D
x 100
C + D
Comments
z
Disease status
Cancer
No cancer
Total
Positive
Negative
132
47
985
62295
1117
62342
Total
179
63280
63459
z
z
z
0.3%
73.7%
98.4%
11.8%
99.9%
PV-
A
x 100
A + B
Predictive values
Mammography
No disease
TEST RESULT
SUMMARY
A screening test study determines the
usefulness of a test in identifying those at
risk of a disease
z Students must be able to calculate and
interpret sensitivity, specificity & predictive
values.
z
THANK YOU
Year-2, Semester-1
Trigger:
You are the State Medical Officer for AIDS/HIV of Negeri Sembilan and you are expected
to conduct a sentinel surveillance for HIV amongst;
o
Page 2 of 12
Year-2, Semester-1
Positive
Negative
Total
Disease
Present
TP
FN
TP + FN
Disease
Absent
FP
TN
FP + TN
Total
TP + FP
FN + TN
N
TP = True Positive
FP = False Positive
FN = False Negative
TN = True Negative
Sensitivity = TP/(TP+FN) x 100%
total
1009
8991
10,000
total
1269
8731
10,000
Rapid Test
+
total
Gold Standard
+
998
180
2
8820
1000
9000
total
1178
8822
10000
+
total
Gold Standard
+
930
180
70
8820
1000
9000
total
1110
8890
10000
EIA
PA
Rapid
Oral
Sensitivity
Specificity
PPV
NPV
Page 5 of 12
Year-2, Semester-1
Disease
Absent
Total
PPV =
NPV =
Positive
10
13
Negative
9987
9987
Total
9997
10000
Disease
Present
Disease
Absent
Total
Positive
10
19
Negative
9981
9981
Total
9991
10000
Disease
Present
Disease
Absent
Total
Positive
2000
2008
Negative
7992
7992
Total
2000
8000
10000
Blood donors
PPV =
NPV =
IVDU
Population
Antenatal mothers
Blood donors
IVDUs
Population with
HIV
3
9
2000
PPV =
Population
without HIV
9987
9991
8000
NPV =
TOTAL
Prevalence rate
10,000
10,000
10,000
Since the sensitivity and specificity is the same for all three study populations, please discuss how
PPV and NPV are affected by the prevalence of the disease in each study population.
PPV and NPV can also be calculated using the following formulas;
PPV =
Prevalence
x
Sensitivity
(Prev x Sen) + (1 - Prev)x (1 - Sp)
Page 6 of 12
Year-2, Semester-1
Population
Sensitivity
Specificity
Prevalence
0.01%
0.02%
0.03%
0.05%
0.09%
1.00%
5.00%
10.00%
20.00%
30.00%
NPV
d/c+d
100.00%
100.00%
100.00%
100.00%
100.00%
100.00%
100.00%
100.00%
100.00%
100.00%
<- Antenatal
<- Blood Donors
prevalence
20.0%
10.0%
5.0%
1.0%
0.1%
99%
99%
96.1%
91.7%
83.9%
50.0%
9.0%
sensitivity %
specificity %
95%
90%
95%
90%
82.6%
69.2%
67.9%
50.0%
50.0%
32.1%
16.1%
8.3%
1.9%
0.9%
80%
80%
50.0%
30.8%
17.4%
3.9%
0.4%
Page 7 of 12
Year-2, Semester-1
References:
Osman Ali. 1990. Kaedah Epidemiologi. Penerbit: Dewan Bahasa Dan Pustaka.
UNAIDS/WHO. 2004. UNAIDS/WHO Policy Statement on HIV Testing
http://www.who.int/ethics/topics/hivtestingpolicy_who_unaids_en_2004.pdf
WHO (March 1997) Revised Recommendation for the Selection and Use of HIV Antibody Tests.
Weekly Epidemiological Record, No. 12. http://www.who.int/docstore/wer/pdf/1997/wer7212.pdf
WHOSEA. 1998. Standard Operating Procedures for Diagnosis of HIV Infection.
http://w3.whosea.org/bct/332/diagnosis1.htm
CDC. 2005. What are the different HIV screening tests available in the U.S.?
http://www.cdc.gov/hiv/pubs/faq/faq8.htm
USFDA. 2006. Donor Screening Assays for Infectious Agents and HIV Diagnostic Assays
http://www.fda.gov/cber/products/testkits.htm
Joseph Hellweg. 2005. Narrative and Secrecy: Sentinel Surveillance and Alternative Epidemiologies of
HIV/AIDS in Northwestern Cte d'Ivoire. Africa Conference 2005: African Health and Illness.
http://www.utexas.edu/conferences/africa/2005/panels/hellweg.html
Trisha Greenhalgh. 1997. How to read a paper: Papers that report diagnostic or screening tests. BMJ
1997;315:540-543 (30 August) http://bmj.bmjjournals.com/cgi/content/full/315/7107/540
Page 8 of 12
PRACTICALS GUIDE
Medicine & Society Module (FF2613)
INTRODUCTION
In this module there will be 4 practical sessions for the research project and statistical exercises.
Students will be guided by the respective lecturer/tutor assigned to each lab.
The schedule for the practical sessions for this semester is as stated below;
DATE
14/07/10
TIME
10.30 12.30
TOPIC
CONTENT
Descriptive Statistics
& Research Project 1
21/07/10
10.30 12.30
Analysis of
Quantitative Data &
Research Project 2
20/08/10
2.30 4.30
Correlation &
Research Project 3
27/08/10
10.30 12.30
20/09/10
24/09/10
2.00 4.00
10.00 12.00
Research Project 5
Practical 1
Descriptive Statistics
Introduction
In the old curriculum, the practical sessions were slotted immediately after the
respective lectures. In the past we had 25 hours of lectures and 8 practical sessions
just for statistics and research methodology. Now we only have 7 hours of lecture and
4 practical sessions for statistics and research methodology in the new curriculum.
Whenever possible, we try to slot the practical sessions according to lectures. But we
cant cover everything; therefore students are also expected to learn on their own.
Please be patient and persists in doing the exercises.
For this session, we are will learn about measures of central tendency and
variability. We use these measures of central tendency and variability to describe the
data that we collected. The measures of central tendency are mean, mode and median.
For variability, it is standard deviation (sd). Kindly refer to your formula sheet or your
books for help.
Measures of Central Tendency for Quantitative Data
1. Write down the formulas for mean in the boxes below;
Basic Formula
2. Calculate the mean, mode and median for the age i of the following respondents;
35 24 36 21 21 20 34 29 37 30 26 27 29 34 33 33 27 25 21 26 32 30 33 36 28 33 19
29 27 29 22 23 31 32 31
Total = ___________
Mean = __________
n = ________
Median = __________
Mode = __________
3. Write down the formulas for standard deviation in the boxes below;
Basic Formula
4. Using the data from Q.2, calculate the standard deviation and variance of the age i
of respondents.
x
x-mean (x-mean)2
19.00
20.00
21.00
21.00
21.00
22.00
23.00
24.00
25.00
26.00
26.00
27.00
27.00
27.00
28.00
29.00
29.00
29.00
Total
x
29.00
30.00
30.00
31.00
31.00
32.00
32.00
33.00
33.00
33.00
33.00
34.00
34.00
35.00
36.00
36.00
37.00
x-mean (x-mean)2
Total
For the following exercise, calculate the mean, mode, median and standard deviation
for both cases and controls. To simplify matters, just fill up the table below;
For cases;
Weight in kg
30.0-39.9
40.0-49.9
50.0-59.9
60.0-69.9
70.0-79.9
80.0-89.9
90.0-99.9
Total
Frequency
5
48
43
10
2
1
1
110
m.p
34.95
44.95
54.95
64.95
74.95
84.95
94.95
f.mp
f.mp2
f cumulative
5
53
96
106
108
109
110
For controls;
Weight in kg
30.0-39.9
40.0-49.9
50.0-59.9
60.0-69.9
70.0-79.9
80.0-89.9
90.0-99.9
Total
Frequency
0
21
39
35
8
2
3
108
m.p
34.95
44.95
54.95
64.95
74.95
84.95
94.95
f.mp
0
f.mp2
0
f cumulative
0
21
60
95
103
105
108
Control
Mean
Mode
+
Median
+
Standard deviation
=
Practical 1b
Research Proposal
Each lab group is required to come up with a research proposal, collect the data
required, analyse the data, present their findings and write up the final report for
submission.
For this session, the students are expected to agree on the;
Title of the research
Objectives
Problem Framework
Hypothesis
Methodology
Once the above has been agreed upon, as homework, they are expected to write up the
proposal, including the questionnaire, which will be discussed during the second
practical session.
Practical 2
Inferential Statistics
Statistical Tests & Types of Variables
In general there are 2 types of variables; qualitative & quantitative. When you want to
test the association between 2 variables, the type of test to be utilised depends on the
type of variables. The tables below gave a general guide on the correct statistical test
for the respective variable types.
Qualitative Data Analysis
Parametric Analysis
Qualitative
Dichotomus
Qualitative
Polinomial
Quantitative
Quantitative
Student's t Test
Quantitative
ANOVA
Quantitative
Quantitative continous
Non-Parametric Analysis
Variable 1
Qualitative
Dichotomus
Qualitative
Dichotomus
Qualitative
Polinomial
Quantitative
Quantitative continous
Variable 2
Qualitative
Dichotomus
Criteria
Type of Test
Sample size < 20 or (< 40 but Fisher Test
with at least one expected value
< 5)
Quantitative Data not normally distributed
Wilcoxon Rank Sum
Test or U MannWhitney Test
Quantitative Data not normally distributed
Kruskal-Wallis One
Way ANOVA Test
Quantitative Repeated measurement of the Wilcoxon Rank Sign
same individual & item
Test
Quantitative - Data not normally distributed
Spearman/Kendall
continous
Rank Correlation
Practical 2
This is the second practical session for this module. In this session, we will be
conducting exercises on Students t-test, paired t-test and proportionate test.
Students t-test
1a. Write down the formula for Students t-test in the boxes below;
Basic Formula
b. Based on results from the previous session, Q5, complete the boxes below;
Case
Control
110
108
Mean
Standard deviation
n
e. Please refer to table A1 and A3, and try to estimate the p value from the t value
calculated. Discuss which table is more appropriate for this exercise.
f. Based on the above p value, is the null hypothesis rejected?
g. Is there a significant difference of first trimester weight between the two groups?
Explain your answer.
2. During the examination, we will not tell you what test to use. Instead the students
are expected to choose the appropriate one based on the problem and the data given.
For example, try to do the exercise below;
A case-control study to identify factors that can cause small for gestational age SGA
was conducted. Among the factors studied were the mothers heights. It is believed
that the shorter mothers were of higher risk to get SGA babies.
Total of samples n
Total of weight x
Total of (x-mean)2
Total of samples n
Total of weight x
Total of (x-mean)2
Case
110
16620
2326
Control
108
16439
3605
Both groups
218
33059
5931
a. State the hypothesis and null hypothesis for the above problem.
Paired t-test
3a. Write down the formula for paired t-test in the box below;
Basic Formula
b. Thirty of the pregnant mothers were found to be anaemic during their second
trimester follow-up. They were treated with haematinics for 2 months and their
haemoglobin levels were measured again. To measure the effectiveness of the
treatment, please complete the table below.
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
Hb1
9.3
9.5
9.5
9.6
9.7
9.8
9.8
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.1
Hb2
9.5
10.0
10.0
11.0
12.0
9.0
9.6
7.2
9.6
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.0
10.3
10.5
10.6
10.8
11.0
11.0
11.0
11.0
11.5
13.0
13.0
13.0
11.0
D2
Total
c. Is the intervention effective? Do a paired t-test analysis using the data above.
Proportionate Test
4a. Write down the formula for proportionate test in the box below;
Basic Formula
The rate of SGA for mothers exposed to cigarette smoke (passive smoker) was
89/156. The rate of SGA for mothers not exposed to cigarette smoke was 20/61.
b. State the appropriate null hypothesis.
c. Do the proportionate test and discuss its result using 0.05 as the level of
significance (the z value in the normal distribution table for 0.05 as the level of
significance is 1.96).
Research Project 2
Presentation of the complete research proposal. Upon acceptance of the proposal, as
homework, the students are expected to distribute the questionnaires and collect the
data for the study. All completed forms are to be brought to the third practical session.
Practical 3
Inferential Statistics 2
Introduction
This is the third practical session. In this session we will do exercises on Pearson
correlation and linear regression.
Pearson Correlation
1a. Write down the formula for Pearson Correlation in the boxes below;
Basic Formula for r
(x-mean x)2
(y-mean y)2
As you can see from the formulas above, to calculate the correlation coefficient (r),
you need to identify the following;
Total of the first variable (x),
Total of the first variable squared (x2),
Total of the second variable (y),
Total of the second variable squared (y2) and
Total of the two variables multiplied (xy).
Just imagine the number of calculations that you have to do before you even get to
calculate the correlation coefficient (r). If the sample size is 150, you will have to do
more than 455 calculations. Since youll be doing this calculations manually, the
chance of error occurring is quite high indeed.
For exercise, complete the following table. Measure the time required to complete it.
Once done, please note that you may have to do the same thing again for a dataset 5
times larger than this..
2.
A case-control study to identify factors that can cause small for gestational age
SGA was conducted.
In the past exercise, we have proven that there is an association between the
mothers first trimester weight and SGA.
Now we want to see whether there is an association between the mothers first
trimester weight (WEIGHT2) and the childs birth weight (BIRTHWGT).
Please complete the following table;
INDEX
9
10
12
20
21
29
31
32
34
43
60
70
72
79
90
97
117
126
131
138
145
146
156
159
171
173
174
175
178
181
TOTAL
WEIGHT2
42.00
40.00
66.00
51.50
47.50
39.50
40.00
46.50
55.00
49.20
45.00
63.50
52.40
52.30
47.50
62.00
55.10
72.00
61.50
86.00
60.80
44.00
58.00
70.00
44.00
59.50
47.50
53.00
62.50
92.00
WEIGHT22
BIRTHWGT
2.40
2.30
2.30
2.10
2.23
2.49
2.46
2.52
2.28
2.20
2.48
2.00
2.31
2.15
2.55
2.41
3.46
3.50
2.97
3.48
3.00
2.84
3.55
3.19
3.09
3.56
3.16
3.10
3.27
3.00
BIRTHWGT2
xy
a. State the null hypothesis for correlation test between the two variables.
b. Conduct the correlation test and calculate the r (correlation coefficient). How
strong is the relationship between the two variables?
Babies' Birthweight
1.8
1.6
1.4
1.2
1.0
.8
.6
r = 0.431, p = 0.017
.4
.2
0.0
Rsq = 0.1874
0
10
20
30
40
50
60
70
80
90
100
Mothers' Weight
To expect the students to calculate all that during the examination, would be
rather cruel. Instead, usually, all the required data will be given, along with some
extraneous data, just to confuse the students. It is up to the students to select the
appropriate data and use it in the appropriate statistical test.
3. A case-control study to identify factors that can cause small for gestational age
SGA was conducted. Among the factors studied were whether there is an
association between the mothers height in cm (HEIGHT) and the childs birth
weight in kilogram (BIRTHWGT).
n = 218
Mean
Standard deviation
(observation)
(observation2)
(observation 1 x observation 2)
HEIGHT
151.65
5.26
33059.00
5019291.00
BIRTHWGT
2.79
0.54
608.46
1760.98
92386.35
a. Name the appropriate statistical test to test the association between the two
variables.
b. State the null hypothesis for the above statistical test.
c. Conduct the statistical test including the test of significance. Discuss the result of
the test.
Linear Regression
4a. Write down the formula for linear regression in the boxes below;
Basic Formula
b. Using the data from Q2, conduct the test for linear regression and calculate the
regression co-efficient (b) and constant (a).
Research Project 3
Students will be guided on how to enter the data that they have collected into the
computer using Excel or SPSS. Each lab is required to prepare a notebook for the
session.
For homework, students are required to complete the data entry for all collected data
and bring the completed file to the fourth practical session.
Hakcipta terpelihara Dr Azmi Mohd Tamil
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