Final Information
Course Semester Type Technology
Permitted materials
SCIE1000 Theory and Practice in Science
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Summer Semester, 2021
Online, non-invigilated assignment, under ‘take home exam’ conditions. File upload to Blackboard Assignment
This assignment is closed book – only specified materials are permitted.
Your assignment will begin at the time specified by your course coordinator. You have a 12-hour window in which you must complete the final assessment. You can access and submit your paper at any time within the 12 hours. Even though you have the entire 12 hours to complete and submit this assessment, the expectation is that it will take students around 2 hours to complete.
Note that you must leave sufficient time to submit and upload your answers.
Recommended materials
Ensure the following permitted materials are available during the final:
• The SCIE1000 lecture book, workshop activities & solutions, and your personal notes from the course (paper or electronic).
• UQ approved calculator; bilingual dictionary; phone/camera/scanner
Instructions
You will need to download the question paper included within the Blackboard Test. Once you have completed the assignment, upload a single pdf file with your answers to the Blackboard assignment submission link. You may submit multiple times, but only the last uploaded file will be graded. Ensure that all your answers are contained in your last uploaded file.
You can print the question paper and write on that paper or write your answers on blank paper (clearly label your solutions so that it is clear which problem it is a solution to) or annotate an electronic file on a suitable device.
You should include your name and student number on the first page of the pdf file that you submit.
For advice / options for producing a PDF file from handwritten work, see the “Electronic Assignment Submission Guidelines” on Blackboard, under the Final tab.
Who to contact
Given the nature of this assessment, responding to student queries and/or relaying corrections during the allowed time may not be feasible.
If you have any concerns or queries about a particular question or need to make any assumptions to answer the question, state these at the start of your solution to that question. You may also include queries you may have made with respect to a particular question, should you have been able to ‘raise your hand’ in an examination-type setting.
If you experience any interruptions, please collect evidence of the interruption (e.g. photographs, screenshots or emails).
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If you experience any technical difficulties, contact Intyre on Note that this is for technical difficulties only.
Late or incomplete submissions
In the event of a late submission, you will be required to submit evidence that you completed the assessment in the time allowed. This will also apply if there is an error in your submission (e.g. corrupt file, missing pages, poor quality scan). We strongly recommend you use a phone camera to take time-stamped photos (or a video) of every page of your paper during the time allowed.
If you submit your paper after the due time, then you should send details to SMP Exams as soon as possible after the end of the time allowed. Include an explanation of why you submitted late (with any evidence of technical issues) AND time-stamped images of every page of your paper (e.g. screen shot from your phone showing both the image and the time at which it was taken).
Further important information
Academic integrity is a core value of the UQ community and as such the highest standards of academic integrity apply to all assessment items, whether undertaken in-person or online.
This means:
• You are permitted to refer to the allowed resources for this assessment item, but you cannot cut-and-paste material other than your own work as answers.
• You are not permitted to consult any other person – whether directly, online, or through any other means – about any aspect of this assessment during the period that it is available.
• If it is found that you have given or sought outside assistance with this assessment, then that will be deemed to be cheating.
If you submit your answers after the end of the allowed time, the following penalties will be applied to your final score due to the late submission:
• Less than 5 minutes – 5% penalty
• From 5 minutes to less than 15 minutes – 20% penalty
• More than 15 minutes – 100% penalty
These penalties will be applied unless there is sufficient evidence of problems with the system and/or process that were beyond your control.
Undertaking this online assessment deems your commitment to UQ’s academic integrity pledge as summarised in the following declaration:
“I certify that I have completed this assessment in an honest, fair and trustworthy manner, that my submitted answers are entirely my own work, and that I have neither given nor received any unauthorised assistance on this assessment item”.
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Summer Semester Final, 2021 SCIE1000 Theory and Practice in Science
To answer each question you will need to use the information on Page 17. Your solutions will be marked on the correctness and clarity of your explanation and communication. Include units in your answer wherever relevant.
Each question is graded on a 1-7 scale with the last part of the question being at an advanced level which must be attempted for students aiming for a grade of 6 or 7.
1. A study of the Aedes aegypti population in Brisbane compiled the estimated number of non- compliant rainwater tanks over the years 1910 to 1970 [1]. The graph below (adapted from [1]) shows biannually reported non-compliant water tanks (in thousands of tanks) over the shorter period of 1950 to 1970. In the questions that follow, we will use N for the number of non- compliant water tanks, and t for time.
30 25 20 15 10
0 2 4 6 8 10 12 14 16 18 20
Years since 1950
(a) A researcher suggests that the data could be modelled by a power law function (with a vertical offset) of the form N = atp + b. For the constants involved (a, p, b), indicate whether each would be positive, negative or zero. Justify your answers by referring to the
scientific context.
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Non-compliant water tanks (1000s)
Summer Semester Final, 2021 SCIE1000 Theory and Practice in Science
(b) Another researcher suggests that an exponential function of the form N = Cekt + b would be a better fit. Again, for the constants involved (C, k, b), indicate whether each would be positive, negative or zero, with appropriate scientific justification. (2 marks)
(c) Would you consider the models proposed in parts (a) and (b) of this question to be phe- nomenological or mechanistic? Explain your reasoning. (1 mark)
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(d) (Advanced) Estimate the total volume of water stored in domestic water tanks in Brisbane in 1960. Explain any assumptions that you make. (2 marks)
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2. A study of outbreaks of the mosquito-transmitted Zika virus was conducted in Brazil from 2015 to 2016 [4]. The number of seasonal human Zika cases was monitored across eight states. The following log-linear graph shows the weekly Zika case numbers recorded in the state of Acre against the time after the first detected case.
(a) Using what you have learned in the philosophy of science component of SCIE1000, explain why the graph shown above can be interpreted as a model. In doing so, refer to specific aspects of the graph. (1 mark)
(b) In the Philosophy of Science module, we discussed a special challenge that models pose for falsificationism. Explain this challenge with reference to the above model. (1 mark)
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(c) Use the graph above to find a linear equation relating the natural logarithm of the number of cases to time. Ensure that you quote values for any constants that you obtain. (3 marks)
(d) (Advanced) Use your equation to find the doubling time for the increase in Zika cases in Acre in this outbreak. Explain the steps you took to achieve this. If you were unable to obtain an equation, then explain the steps that would be involved. (2 marks)
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3. Consider a simple model of the life stages of Aedes aegypti in which we consider three stages — egg (E), water-based larva/pupa (L), and winged adult mosquito (M). The following is known about each of the stages:
• Eggs hatch only when submerged in water, but can survive for many months in a dry state. In this model, we will consider the average time from laying to hatching to be 5 days, and hence that 20% of eggs hatch per day.
• To account for the fact that only a certain proportion of eggs laid will actually hatch, we will consider that every day, 10% of the existing eggs become no longer viable.
• The larva/pupa stage lasts for 7 days, with a survival rate of 70% per day.
• Adults live for 20 days.
• Females produce on average 150 eggs per batch, and lay three batches during their lifetime.
(a) The following incomplete life-cycle diagram represents the stages of growth of Aedes aegypti. Using the information provided, complete the life cycle diagram by labelling the arrows appropriately assuming rate changes are per day. (3 marks)
ELM die die die
(b) Develop a set of differential equations for the life stages based on the life-cycle diagram. If you were unable to complete part (a) then just introduce appropriate constants (a, b, …)
for each unknown rate.
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(c) (Advanced) Discuss two approaches that can be used to control the population of Aedes aegypti. Explain how your differential equations could be adapted to account for each
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4. A study of the spread of mosquitos in city blocks used numerical approaches to model the population dynamics of Aedes aegypti [5]. Although the model accounted for the movement of mosquitoes across multiple blocks, we can use their approach to model the development of the mosquito population in a single city block. They created two differential equations to describe the change in the population of the aquatic (A) stage of life and the adult winged mosquito (M) stage of life:
′M M=γ1−k A−μMM
′A A=r1−k M−(μA+γ)A
Here γ = 0.2 day−1 is the rate of maturation of the aquatic phase into the winged phase, μM = 0.04 day−1 is the mortality rate of the winged phase, r = 30 day−1 is the rate at which mosquito eggs are laid, and μA = 0.01 day−1 is the mortality of the aquatic phase. Quoted values for kM and kA are 25 and 100 respectively.
(a) Assumingstartingpopulationsoftwomosquitoesintheadultwingedstageand10mosquitoes in the aquatic stage, use Euler’s method and a step size of 1 day to calculate the new pop- ulation of mosquitoes in the adult winged phase after two days. (4 marks)
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(b) Explain the physical significance of the constants kM and kA used in this model. (1 mark)
(c) (Advanced) At large times, the model predicts that the populations of both stages are approximately constant. If the number of mosquitoes in the aquatic stage is found to be constant at 97, what constant population would be in the adult winged stage? Comment on these values in relation to relevant constants used in the modelling and the scientific
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Summer Semester Final, 2021 SCIE1000 Theory and Practice in Science
5. In a study on dengue and malaria in South-East Asia, the exposure of workers to disease-carrying mosquitoes in villages, rubber plantations and forests was investigated [6]. The following table (adapted from [6]) relates to the exposure of migrant workers that live and work in rubber plantations. It shows the average number of female mosquitoes that each worker encounters per hour over a 24-hour period (measured using a mosquito trap).
Time(hours) 0 5 7 11 17 20 24 Mosquitoes (per hour) 0 0 0.4 0.3 1.1 0 0
(a) Using the axes below (or draw your own), make a plot of time (horizontal axis) against the number of mosquitoes per hour (vertical axis) using the information given in the table. Join data points using straight lines. Divide relevant regions into trapezoids and label these regions numerically (1, 2, 3 . . . ). Ensure your graph is appropriately communicated.
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(b) Determine the total exposure to disease-carrying mosquitoes for each rubber plantation worker over the 24-hour period using the trapezoid rule. Explain the meaning of the value that you calculate. (3 marks)
(c) (Advanced) Villagers who work in the local forests encounter, on average, 1.5 mosquitoes per hour when working from 6 am until 5 pm each day. Which of the two populations (migrants in rubber plantations or villagers in the forests) experience a higher exposure to dengue (carried by mosquitoes), and by what factor? (2 marks)
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6. The basic reproduction number, R0, is defined as the expected number of secondary infections generated by one infective person in a fully susceptible population. For the spread of the dengue virus, an equation for R0 can be calculated by taking into consideration multiple factors including mosquito density, daily bite rate, and transmission rate between humans and mosquitoes [7]. Using typical values for many of the parameters, it is possible to write a simplified equation in the form
R0 = 0.23Me−6.7μ μ
Here M is the relative density of female mosquitoes per person (assumed constant), and μ is the mortality rate per day of the mosquitoes. The latter parameter can be controlled by, for example, the use of insecticides at regular intervals. The following Python code relates to this equation.
# Dengue calculations
from pylab import *
# Functions
def fdash(M,mu):
return (-0.23 * M * exp(-6.7 * mu) * (1 / mu ** 2 + 6.7 / mu))
def f(M,mu):
return (0.23 * M * exp(-6.7 * mu) / mu) – 1
M_in = float(input(“Mosquitoes: “)) val = float(input(“Initial guess: “)) # Loop
while abs(f(M_in, val)) > 0.0001:
val = val – f(M_in,val) / fdash(M_in, val) i=i+1
print(“Step”, i, “:”, round(val,3))
(a) The code is run once with the input of 1.5 mosquitoes and an initial guess of 0.1. Determine the output for one iteration of the while loop. Ensure that you show all working. (3 marks)
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(b) The communication in the code is poor. Suggest one change to improve the communication within the code (giving an example), and one change to improve the communication with the user (also with an example). (2 marks)
(c) (Advanced) The code executes multiple times giving a final output value of 0.137. Explain the physical significance of this value in relation to the basic reproduction number and
spread of the disease.
END OF QUESTIONS
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References
[1] Trewin, B.J., Darbro, J.M., Jansen, C.C., Schellhorn, N.A., Zalucki, M.P., Hurst, T.P, Devine, G.J. (2017) The elimination of the dengue vector, Aedes aegypti, from Brisbane, Australia: The role of surveillance, larval habitat removal and policy. PLOS Neglected Tropical Diseases 11(8), e0005848.
[2] Chung, H.-N. et al. (2018) Toward Implementation of Mosquito Sterile Insect Technique: The Effect of Storage Conditions on Survival of Male Aedes aegypti Mosquitoes (Diptera: Culicidae) During Transport. Journal of Insect Science 18(6): 2, 1–7.
[3] Crawford, J.E. et al. (2020) Efficient production of male Wolbachia-infected Aedes aegypti mosquitoes enables large- scale suppression of wild populations. Nature Biotechnology 38, 482–492.
[4] Zhao,S.,Musa,S.S.,Fu,H.,He,D.,Qin,J.(2019)Simpleframeworkforreal-timeforecastinadata-limitedsituation: the Zika virus (ZIKV) outbreaks in Brazil from 2015 to 2016 as an example. Parasites Vectors 11, 245–258.
[5] Yamashita, W.M.S., Das, S.S., Chapiro, G. (2018) Numerical modeling of mosquito population dynamics of Aedes aegypti. Parasites Vectors 12, 344–356.
[6] Tangena, J-A.A., Thammavong, P., Lindsay, S.W., Brey, P.T. (2017) Risk of exposure to potential vector mosquitoes for rural workers in Northern Lao PDR. PLOS Neglected Tropical Diseases 11(7), e0005802.
[7] Coelho, F.C., Codeco, C.T., Struchiner, C.J. (2008) Complete treatment of uncertainties in a model for dengue R0 estimation. Cad. , Rio de Janeiro 24(4), 853–861.
Space for further working (if needed) . . .
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Information on Aedes aegypti
Aedes aegypti is a type of mosquito found in tropical countries, including Australia. These mosquitoes typically live and breed in urban areas, and female mosquitoes feed predominantly on humans [1]. Mosquitoes lay eggs that can remain dormant for extended periods, but hatch when a suitable aquatic environment arises (such as after heavy rain). The resulting larvae grow to become pupae (both aquatic stages) before developing into adults. Adult mosquitoes are responsible for the transmission of a range of diseases including dengue, Zika, and chikungunya. Outbreaks of such diseases regularly occur in regions where Aedes aegypti mosquitoes are found. Control and eradication is thus extremely important.
There are various methods for controlling or eradicating Aedes aegypti. Three specific approaches are:
• Minimising the availability of water and thus a suitable aquatic environment for eggs to hatch
and become larvae.
• Using insecticides to periodically kill adult mosquitoes.
• Releasing sterilised male mosquitoes into the infested area. The mating of wild females with the sterilised males does not produce viable eggs, and the population eventually declines. Sterilisation can be by irradiation, genetic modification, or the introduction of the Wolbachia bacteria into the male mosquitoes before release [2, 3].
Eradication from Brisbane:
In the early 1900s, Aedes aegypti populations were widespread across Australia, extending almost as far south as the Victorian border [1]. Several dengue epidemics occurred, resulting in many hundreds of deaths. In the mid-1900s, Aedes aegypti populations were observed to decline, and modelling indicated that Aedes aegypti was completely eliminated from Brisbane around 1960 (at a time when Brisbane had around 600,000 residents).
One aspect that was thought to assist with this eradication was the reduction in the number of do- mestic rainwater tanks that could be potential breeding locations for mosquitoes [1]. Regulations were introduced that required all water tanks to be compliant such that mosquitoes could not enter and lay eggs in the tanks. Regular checks were made to ensure that these regulations were being followed also allowing the collection of data about non-compliant tanks and mosquito populations. In the 1940s, just about every house had a rainwater tank but, by 1960, only around 20% of households continued to have a water tank (and 90% of these tanks were m
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