AMED3003: Semester 2, 2022

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Units AMED3003 Semester 2 2022 [Normal day]

Unit of study_

AMED3003: Diagnostics and Biomarkers

Semester 2, 2022 [Normal day] - Westmead, Sydney

Overview

Diagnostic sciences have evolved at a rapid pace and provide the cornerstone of our health care system. Effective diagnostic assays enable the identification of people who have, or are at risk of, a disease, and guide their treatment. Research into the pathophysiology of disease underpins the discovery of novel biomarkers and in turn, the development of revolutionary diagnostic assays that make use of state-of-the-art molecular and cellular methods. In this unit you will explore a diverse range of diagnostic tests and gain valuable practical experience in a number of core diagnostic methodologies, many of which are currently used in hospital laboratories. Together we will also cover the regulatory, social, and ethical aspects of the use of biomarkers and diagnostic tests and explore the pathways to their translation into clinical practice. By undertaking this unit, you will develop your understanding of diagnostic assays and biomarkers and acquire the skills needed to embark on a career in diagnostic sciences.

Unit details and rules

Unit code	AMED3003
Academic unit	Department of Medical Sciences
Credit points	6
Prohibitions ?	AMED3903
Prerequisites ?	12cp from (IMMU2101 or MEDS2004 or MIMI2002 or MIMI2902 or PHSI2005 or PHSI2905 or PHSI2006 or PHSI2906 or PHSI2007 or PHSI2907 or MEDS2001 or PCOL2011 or PCOL2021 or MEDS2002 or BCMB2001 or BCMB2901 or MEDS2003) or [BMED2401 and 6cp from (BMED2402 or BMED2403 or BMED2404 or BMED2405 or BMED2406)]
Corequisites ?	None
Assumed knowledge ?	None
Available to study abroad and exchange students	Yes

Teaching staff

Coordinator	Fabienne Brilot-Turville, fabienne.brilot@sydney.edu.au
Lecturer(s)	Fabienne Brilot-Turville, fabienne.brilot@sydney.edu.au

Type	Description	Weight	Due	Length
Final exam (Open book)	Open Book Exam SAQs, critical thinking, data analysis	30%	Formal exam period	1 hour
Outcomes assessed:
Tutorial quiz	Quiz and participation (workshops) short Quiz at most workshops participation for some workshops	10%	Multiple weeks	10 minutes for each quiz
Outcomes assessed:
Presentation	Assignment 1: Illustrator schematic and oral presentation Illustrator schematic and oral presentation-individual	30%	Please select a valid week from the list below	Oral presentation of ~6 min (Pecha Kucha
Outcomes assessed:
Assignment	Assignment 2: POSTER Poster: data analysis and graphing, data discussion, Illustrator schematic	30%	Week 13 Due date: 31 Oct 2022 at 23:00	~500 words
Outcomes assessed:
= Type C final exam ?

Assessment summary

Tutorial quizzes and participation – short quiz at most workshops and participation for some workshops – individual
Assignment 1: Illustrator schematic and Pecha Kucha presentation – Illustrator schematic and 1 Pecha Kucha presentation – individual
Assignment 2: Poster based on Practical: report, data analysis and graphing, data discussion, Illustrator schematic – individual
Open Book Exam – SAQs, critical thinking, data analysis – individual

Further details can be found on the unit’s Canvas page.

Assessment criteria

The University awards common result grades, set out in the Coursework Policy 2014 (Schedule 1).

As a general guide, a high distinction indicates work of an exceptional standard, a distinction a very high standard, a credit a good standard, and a pass an acceptable standard.

For more information see sydney.edu.au/students/guide-to-grades.

For more information see guide to grades.

Late submission

In accordance with University policy, these penalties apply when written work is submitted after 11:59pm on the due date:

Deduction of 5% of the maximum mark for each calendar day after the due date.
After ten calendar days late, a mark of zero will be awarded.

Academic integrity

The Current Student website provides information on academic integrity and the resources available to all students. The University expects students and staff to act ethically and honestly and will treat all allegations of academic integrity breaches seriously.

We use similarity detection software to detect potential instances of plagiarism or other forms of academic integrity breach. If such matches indicate evidence of plagiarism or other forms of academic integrity breaches, your teacher is required to report your work for further investigation.

You may only use artificial intelligence and writing assistance tools in assessment tasks if you are permitted to by your unit coordinator, and if you do use them, you must also acknowledge this in your work, either in a footnote or an acknowledgement section.

Studiosity is permitted for postgraduate units unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission.

Learning support

Simple extensions

If you encounter a problem submitting your work on time, you may be able to apply for an extension of five calendar days through a simple extension.  The application process will be different depending on the type of assessment and extensions cannot be granted for some assessment types like exams.

Special consideration

If exceptional circumstances mean you can’t complete an assessment, you need consideration for a longer period of time, or if you have essential commitments which impact your performance in an assessment, you may be eligible for special consideration or special arrangements.

Special consideration applications will not be affected by a simple extension application.

Using AI responsibly

Co-created with students, AI in Education includes lots of helpful examples of how students use generative AI tools to support their learning. It explains how generative AI works, the different tools available and how to use them responsibly and productively.

Weekly schedule

WK	Topic	Learning activity
Week 01	Uos introduction and group work	Workshop (2 hr)
Week 02	Newborn Screening and introduction to Illustrator	Workshop (2 hr)
Week 03	Tracking disease and disease surveillance	Workshop (2 hr)
Week 03	Laboratory practical 1 (online)	Practical (5 hr)
Week 04	Prenatal Diagnosis and post natal management	Workshop (2 hr)
Week 05	Schematic representation of a concept	Workshop (2 hr)
Week 05	Laboratory practical 2 (LIVE and online)	Practical (5 hr)
Week 06	Normal range, accuracy and precision in diagnostic	Workshop (2 hr)
Week 07	Gold standard, sensitivity and specificity in diagnostics	Workshop (2 hr)
Week 08	How to plot data and data analysis	Workshop (2 hr)
Week 09	Oral presentations	Workshop (2 hr)
Week 10	Bad biomarkers and unorthodox diagnostic tests	Workshop (2 hr)
Week 11	Method validation from biomarker to diagnostic and regulatory framework	Workshop (2 hr)
Week 11	Laboratory Practical 3 (LIVE and online)	Practical (5 hr)
Week 12	Antibody detection and analysis	Workshop (2 hr)
Week 13	Debate and exercises	Workshop (2 hr)

Attendance and class requirements

Attendance:

All ZOOM sessions are synchroneous and AMED3003/3903 UoS are not based on an “on-demand” learning. Workshop are interactive and high level of participation is needed to get the most of this kind of teaching. Many workshops include exercises and data analysis, and results are discussed with the class.

Unless otherwise indicated, students are expected to attend a minimum of 80% of timetabled activities for a unit of study, unless granted exemption by the Associate Dean.

For some units of study the minimum attendance requirement, as specified in the relevant table of units or the unit of study outline, may be greater than 80%.

The Associate Dean may determine that a student has failed a unit of study because of inadequate attendance.

Requirements:

An electronic BYO device that you can type on (e.g. laptop).

Access to Illustrator software: Adobe Creative Cloud is available on campus - Library or Learning Hubs (https://www.sydney.edu.au/students/study-spaces.html). You can

book pods or computers in our learning hubs . Bookings can be made for up to four hours, twice a day, 8am to 9pm Monday to Friday.

Adobe Creative Cloud is also available on laptops that can be rented in Building K on Westmead campus.

Adobe Creative Cloud is also available on desktops in the Westmead Hospital Library on Westmead campus.

Alternatively, Adobe Creative Cloud is available for $45 for 1 year license offer at https://sydney.edu.au/epay. Please allow several days to receive the license.

Access to Prism GraphPad software (free download via USYD ICT website). Free access will be based on student enrollment in AMED3003 and 3903. The access to the software will be given to students during Week 1-3.

Access to EndNote software (free download via USYD ICT).

Study commitment

Typically, there is a minimum expectation of 1.5-2 hours of student effort per week per credit point for units of study offered over a full semester. For a 6 credit point unit, this equates to roughly 120-150 hours of student effort in total.

Learning outcomes

Learning outcomes are what students know, understand and are able to do on completion of a unit of study. They are aligned with the University's graduate qualities and are assessed as part of the curriculum.

Outcomes
Graduate qualities

At the completion of this unit, you should be able to:

LO1. investigate the biological processes underlying the discovery of viable biomarkers that lead to the diagnosis of disease
LO2. evaluate the characteristics of biomarkers that make them suitable for use as diagnostic tools
LO3. compare and contrast the key tests that are used to diagnose and track the course of disease
LO4. demonstrate competence in a variety of clinical diagnostic techniques
LO5. assess data from key technologies and design strategies to improve outcomes
LO6. analyse the development of advanced diagnostic technologies and critique the scientific basis for their application
LO7. create a translational pathway for a biomarker or a diagnostic assay
LO8. apply quality assurance and audit tools as well as national regulatory and ethical standards in the application of medical sciences to the clinical environment.

Graduate qualities

The graduate qualities are the qualities and skills that all University of Sydney graduates must demonstrate on successful completion of an award course. As a future Sydney graduate, the set of qualities have been designed to equip you for the contemporary world.

GQ1	Depth of disciplinary expertise Deep disciplinary expertise is the ability to integrate and rigorously apply knowledge, understanding and skills of a recognised discipline defined by scholarly activity, as well as familiarity with evolving practice of the discipline.
GQ2	Critical thinking and problem solving Critical thinking and problem solving are the questioning of ideas, evidence and assumptions in order to propose and evaluate hypotheses or alternative arguments before formulating a conclusion or a solution to an identified problem.
GQ3	Oral and written communication Effective communication, in both oral and written form, is the clear exchange of meaning in a manner that is appropriate to audience and context.
GQ4	Information and digital literacy Information and digital literacy is the ability to locate, interpret, evaluate, manage, adapt, integrate, create and convey information using appropriate resources, tools and strategies.
GQ5	Inventiveness Generating novel ideas and solutions.
GQ6	Cultural competence Cultural Competence is the ability to actively, ethically, respectfully, and successfully engage across and between cultures. In the Australian context, this includes and celebrates Aboriginal and Torres Strait Islander cultures, knowledge systems, and a mature understanding of contemporary issues.
GQ7	Interdisciplinary effectiveness Interdisciplinary effectiveness is the integration and synthesis of multiple viewpoints and practices, working effectively across disciplinary boundaries.
GQ8	Integrated professional, ethical, and personal identity An integrated professional, ethical and personal identity is understanding the interaction between one’s personal and professional selves in an ethical context.
GQ9	Influence Engaging others in a process, idea or vision.

Outcome map

Learning outcomes	Graduate qualities
Learning outcomes

Responding to student feedback

This section outlines changes made to this unit following staff and student reviews.

- Assessments have been streamlined; the second lab report has been replaced by a poster which is a more authentic way to present lab data. - An introduction session to Illustrator has been included in Week 2, so students can start to familiarize themselves with the software. - Some assessment dates have been placed earlier in the semester (week 7 and 9) to allow better spread of the submitted work.

Additional information

Other requirements for this unit include:

Laptop
Lab coat and closed-toe shoes for laboratory practicals - look in lab list
GraphPad Prism and EndNote to be downloaded on students’ laptop (access via USYD).
Access to Adobe Illustrator software

More information can be found on Canvas.

Science student portal:

Work, health and safety

We are governed by the Work Health and Safety Act 2011, Work Health and Safety Regulation 2011 and Codes of Practice. Penalties for non-compliance have increased. Everyone has a responsibility for health and safety at work. The University’s Work Health and Safety policy explains the responsibilities and expectations of workers and others, and the procedures for managing WHS risks associated with University activities.

General Laboratory Safety Rules

No eating or drinking is allowed in any laboratory under any circumstances
A laboratory coat and closed-toe shoes are mandatory
Follow safety instructions in your manual and posted in laboratories
In case of fire, follow instructions posted outside the laboratory door
First aid kits, eye wash and fire extinguishers are located in or immediately outside each laboratory
As a precautionary measure, it is recommended that you have a current tetanus immunisation. This can be obtained from University Health Service: unihealth.usyd.edu.au/

Disclaimer

The University reserves the right to amend units of study or no longer offer certain units, including where there are low enrolment numbers.

To help you understand common terms that we use at the University, we offer an online glossary.

Current students

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Work, health and safety

Disclaimer

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