ARC CENTRE OF EXCELLENCE FOR INTEGRATIVE BRAIN FUNCTION

Mid-Year Research Report 2015

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ARC CENTRE OF EXCELLENCE FOR INTEGRATIVE BRAIN FUNCTION

-Tuesday 18 August -

12:00 - 5:00pm – CIBF ECR Workshop

Pullman Cairns International (17 Abbott St, Cairns)

Attendees:CIBF Scholars & Fellows

ECR Workshop
Location: Boardroom 2
12:00 – 1:00 / Lunch
1:00 – 1:15 / Introduction – Jason Mattingley
1:15 – 2:45 / Facilitating Lab Exchanges – All ECR’s
Introduction to ECR’s, their labs and their projects
2:45 – 3:15 / Afternoon Tea
3:15 – 4:00 / ECR Committee – All ECR’s
Development of Terms of Reference
Development of programs & outcomes
Voting on committee roles
4:00 – 5:00 / Roadmaps For A Successful Science Career – Marta Garrido, EhsanArabzadeh, Jason Mattingley, Gary Egan
Round tables with CI’s to discuss career planning, research strategies, recognising opportunities, overcoming setbacks.
5:00 / Close

5:30 - 10:00pm – CIBF Welcome Dinner

Pullman Reef Hotel Casino (35-41 Wharf St, Cairns)

Attendees:CIBF CI’s, AI’s, Coordinators, Scholars, Fellows, Node Administrators and Advisory Board Members

Welcome Dinner
The Coral Lounge & Pool Deck
5:30 – 6:30 / Welcome drinks
6:30 – 10:00 / Dinner

- Wednesday 19 August -

9:00 - 5:00pm – CIBF Science Meetings

Pullman Reef Hotel Casino (35-41 Wharf St, Cairns)

Attendees:CIBF CI’s, AI’s, Coordinators, Scholars, Fellows, Node Administrators and Advisory Board Members

Main Science Meeting
Location: Urchins 2 & 3
9:00 – 10:30 / Introduction and Overview of CIBF Activities
9:00 – 9:20 / Welcome and overview of recent CIBF activities, Gary Egan
9:20 – 9:40 / Operations update, Lisa Hutton
9:40 – 9:50 / Education and ECR programs, Elizabeth Paton
9:50 – 10:00 / Gender equity, Elizabeth Paton
10:00 – 10:15 / The Brain Dialogue, Rachel Nowak
10:15 – 10:30 / Computation program, WojtekGoscinskiPulin Gong
10:30 – 11:00 / Morning Tea
11:00 – 12:00 / Science Session 1 – Systems (human) neuroscience, Chaired by Michael Breakspear
11:00 – 11:15 / Rapid information processing in subcortical amygdala pathways, Marta Garrido
11:15 – 11:30 / Stimulating connections: an effective connectivity brain map, Gary Egan
11:30 – 11:45 / Understanding human attention, decision-making and prediction using psychophysics, brain imaging and neural stimulation, Jason Mattingley
11:45 – 12:00 / Unified Neural Models for Attention, Prediction and Decision, TaherehBabaie, Peter Robinson
12:00 – 12:30 / Science Session 2 – Spatial Systems (atlases), Chaired by Gary Egan
12:00 – 12:15 / DTI/MRI atlas of the rat brain, Emma Schofield, George Paxinos
12:15 – 12:30 / A digital atlas of connections in the marmoset brain, PiotrMajka, Marcello Rosa
12:30 – 1:30 / Lunch
1:30 – 2:45 / Science Session 3 – Circuits & Cells (animal models), Chaired by Paul Martin
1:30 – 1:45 / Predictive coding as a theory of integrative brain function, with application to the cortical microcircuit, Michael Ibbotson
1:45 – 2:00 / The role of predictive coding in receptive field formation in visual cortex, Hamish Meffen, Michael Ibbotson
2:00 – 2:15 / Sensory decision-making in rodents, EhsanAbrabzadeh & Greg Stuart
2:15 – 2:30 / Visual signal processing in thalamocortical loops; predictive coding in attentional circuit, Paul Martin
2:30 – 2:45 / Neural circuits that mediate fear learning and extinction, Roger Marek, PankajSah
2:45 – 3:30 / Science session 4 – Models & Technology projects – Chaired by Peter Robinson
2:45 – 3:00 / Computer Modelling of Human Visual System with Applications in Computer Vision, Gary Egan, Arthur Lowery
3:00 – 3:15 / Nano Scale Interfaces to Neurons, Stan Skafidas
3:15 – 3:30 / Real time analysis of network function using an all optical interface, Tim Karle, Steve Petrou
3:30 – 4:00 / Afternoon Tea
4:00 – 5:00 / Wrap up and future directions
4:00 – 4:30 / Science program discussion, Gary Egan
4:30 – 4:40 / Industry engagement, Gary Egan
4:40 – 4:50 / International collaborations, Lisa Hutton
4:50 – 5:00 / Concluding comments Gary Egan
5:00 / Close

9:00 - 5:00pm – CIBF Node Administration Meeting

Pullman Reef Hotel Casino (35-41 Wharf St, Cairns)

Attendees:CIBF Management & Node Administrators

Main Science Meeting
Location: Urchins 2 & 3
9:00 – 10:30 / Introduction and Overview of CIBF Activities
9:00 – 9:20 / Welcome and overview of recent CIBF activities, Gary Egan
9:20 – 9:40 / Operations update, Lisa Hutton
9:40 – 9:50 / Education and ECR programs, Elizabeth Paton
9:50 – 10:00 / Gender Equity, Elizabeth Paton
10:00 – 10:15 / The Brain Dialogue, Rachel Nowak
10:15 – 10:30 / Computation, WojtekGoscinskiPulin Gong
10:30 – 11:00 / Morning Tea
11:00 – 3:30 / Node Administration Meeting, Location: Chill out room
11:00 – 11:30 / Administration Session 1 – Getting to know you, Lisa Hutton
Informal round table - who we are, what brought us to this role and what we do in the role
11:30 – 12:30 / Administration Session 2 – Database & Reporting, Lisa Hutton
Overview of database model: input, instructions & expectations
12:30 – 1:30 / Lunch
1:30 – 2:15 / Administration Session 3 – Central & Node Staff Responsibilities, Vicki McAuliffe
Review of roles and responsibilities of central theme and node administrators
2:15 – 3:15 / Administration Session 4 – Information For Node Administrators, Vicki McAuliffe & Elizabeth Paton
Communication to/ from central theme
Policies & procedures
3:15 – 3:30 / Wrap up & Meeting Close
3:30 – 4:00 / Afternoon Tea
4:00 – 5:00 / Main Meeting, Location: Urchins 2 & 3
4:00 – 5:00 / Wrap up and future directions
4:00 – 4:30 / Science program discussion, Gary Egan
4:30 – 4:40 / Industry engagement, Gary Egan
4:40 – 4:50 / International collaborations, Lisa Hutton
4:50 – 5:00 / Concluding comments Gary Egan
5:00 / Close

5:30 - 10:00pm – CIBF Advisory Board Meeting

Pullman Reef Hotel Casino (35-41 Wharf St, Cairns)

Attendees:CIBF Advisory Board Members

Location: Wharf Street Boardroom
5:30 – 10:00 / Advisory Board meeting & working dinner

ARC CENTRE OF EXCELLENCE FOR INTEGRATIVE BRAIN FUNCTION

TABLE OF CONTENTS

1Letter from the Director

2CIBF Personnel...... 3

Chief Investigators (CIs)...... 3

Partner Investigators (PIs)...... 4

Associate Investigators (AIs)...... 4

Coordinators...... 5

Fellows...... 5

Scholars...... 6

Management & Node Administrators...... 6

Advisory Board...... 6

Centre Contributors - Fellows...... 7

Centre Contributors - Scholars...... 8

3CIBF Research projects...... 9

Project 1: Stimulating connections: an effective connectivity brain map...... 10

Project 2: Predictive coding as a theory of integrative brain function, with application to the cortical microcircuit 12

Project 3: The role of predictive coding in receptive field formation in visualcortex...... 14

Project 4: Brain machine interface tiles...... 16

Project 5: Pedunculotegmental nucleus...... 18

Project 6: DTI/ MRI Atlas of the rat brain...... 20

Project 7: Real time analysis of network function using an all optical interface...... 22

Project 8: Unified neural models for attention prediction and decision...... 24

Project 9: Neural signatures of decision making in the primate cortex...... 26

Project 10: Nano scale interfaces to neurons...... 28

Project 11: Sensory decision-making in rodents...... 30

Project 12: Understanding human attention, decision-making and prediction using psychophysics, brain imaging and neural stimulation 32

Project 13: Rapid information processing in subcortical amygdala pathways...... 34

Project 14: Computer modelling of human visual system with applications in computer vision...... 36

Project 15: A digital atlas of connections in the marmoset brain...... 38

Project 16: Visual signal processing in thalamocortical loops; predictive coding in attentional circuits.39

Project 17: Neural circuits that mediate fear learning and extinction...... 40

4CIBF Strategic initiative projects...... 41

SIP 1: Direct assessment of predictive coding as a theory of Integrative brain function...... 42

SIP 2: Nexpo system for experimental interface and data visualisation...... 43

SIP 4: Predictive coding: Clarity imaging of thalamocortical circuits...... 44

SIP 5: Computing facility for modelling...... 45

SIP 6: A custom-designed TMS-compatible headcoil for human brain imaging experiments on attention, prediction and decision-making 46

SIP 9: CLARITY and Viral Vectors to Trace Connections in Attention Pathways...... 47

SIP 10: Endocannabinoid modulation of neuronal excitability...... 48

5Education...... 49

6The Brain Dialogue...... 50

7Neuroinformatics...... 52

8Gender Equity...... 54

9Notes...... 55

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ARC CENTRE OF EXCELLENCE FOR INTEGRATIVE BRAIN FUNCTION

1Letter from the Director

Welcome to the ARC Centre of Excellence for Integrative Brain Function (CIBF) 2015 Science Meeting! I am delighted to report that CIBF has continued to develop during the first half of 2015, in both research activities and the number of researchers associated with the Centre.In the 12 months since the establishment of CIBF in mid 2014, the Centre has become recognised as a nationally important brain research organisation. During 2015 CIBF has grown substantially with the appointment of 24 Centre (post-doctoral and early career research) Fellows and 10 Centre (post-graduate) Scholars who are supported (either wholly or in part) from the Centre, as well as 37 fellows and 36 scholars who are contributing to the Centre’s research programs and activities.

The CIBF 2015 Science Meeting is being held in Cairns in conjunction with the 2015 Australasian Neuroscience Society annual scientific meeting, and the International Neuroinformatics Coordinating Facility (INCF) 2015 annual congress. The Science Meeting will include a comprehensive overview of the Centre’s research output that has been achieved over the past year, together with updates on the experimental and theoretical neuroscience work currently underway, and discussions of the research plans for the next 12 months.

This year the Science Meeting includes an early career research (ECR) half day program of activities. The Centre’s ECRs, fellows and scholars are a critical part of the centre’s future as well as the future of brain research in Australia. I am personally committed to ensuring that CIBF is very active in supporting the next generation of researchers with additional events and activities throughout the life of the Centre.

The collective research productivity from CIBF in 2014 was substantial with over 49 peer reviewed articles, books and book chapters published, and over 20 peer reviewed papers have been published to date in 2015. This provides an excellent basis for discussions at this science meeting that focus on the integration of the research efforts of the four research themes investigating the three fundamental integrative brain function.

I would like to thank Lyn Beazley,Chair of the CIBF Advisory Board, for her continuing support of CIBF during 2015. I would also like to thank the advisory board members, and in particular the international members, for their governance and oversight of the research program and other activities of the Centre. I would also like to acknowledge the hard work of Lisa Hutton, CIBF Centre Manager, the Central Theme, and the CIBF node administrators who have worked tirelessly over the past few months in preparation for the science meeting. The success of the meeting will be in no small part due to their stellar efforts.

The CIBF Executive consists of the CIBF Deputy Director, Marcello Rosa, the CIBF Research Theme leaders, Jason Mattingley, Pankaj Shah, Greg Stuart and Peter Robinson, the Centre Manager, Lisa Hutton, and George Paxinos and Michael Ibbotson, who meet monthly to oversee the management and development of the Centre. The Executive’s work is ensuring the successful establishment of an outstanding brain research program across the CIBF multidisciplinary research environment. Their contributions are ensuring that the scientific goals and broader social outcomes of the Centre are being achieved, and I sincerely thank them for their invaluable work.

A key enabling strategy of the Centre has been the establishment of a computational neuroscience and modelling capability. This consists of access to high performance computing and data storage resources which is co-ordinated by WojtekGoscinski, and a repository of computational modelling tools that is being developed by Pulin Gong.

The Centre has developed a highly successful knowledge sharing program, The Brain Dialogue led by Rachel Nowak, and the Education and ECR program, lead by Ramesh Rajan and supported by Elizabeth Paton, that will be presented during the Science Meeting. I encourage all CIBF investigators, fellows and scholars to actively engage in these programs.

Director, CIBF

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ARC CENTRE OF EXCELLENCE FOR INTEGRATIVE BRAIN FUNCTION Personnel

2CIBF Personnel

Chief Investigators (CIs)

/ Gary Egan
CIBF Director,
Monash University / / Marcello Rosa
Deputy Director,
Monash University / / Jason Mattingley
CI, Theme Leader - Brain Systems,
University of Queensland
/ Peter Robinson
CI, Theme Leader-Modelling & Neurotechnology,
University of Sydney / / PankajSah
CI, Theme Leader- Neuronal Circuits,
University of Queensland / / Greg Stuart
CI, Theme Leader- Cells & Synapses,
Australian National University
/ EhsanArabzadeh
CI,
Australian National University / / Marta Garrido
CI,
University of Queensland / / Ulrike Grünert
CI,
University of Sydney
/ Michael Ibbotson
CI,
University of Melbourne / / Arthur Lowery
CI,
Monash University / / Paul Martin
CI,
University of Sydney
/ George Paxinos
CI,
University of NSW / / Steve Petrou
CI,
University of Melbourne / / Stan Skafidas
CI,
University of Melbourne
/ Michael Breakspear
CI,
QIMR Berghofer Medical ResearchInstitute

Partner Investigators (PIs)

  • Mathew Diamond– InternationalSchool for Advanced Studies (SISSA), Trieste, Italy

  • Sean Hill – International Neuroinformatics Coordinating Facility; theBlue Brain Project;the Human Brain Project, Stockholm, Sweden

  • Viktor Jirsa– Aix-Marseille University, Marseille, France

  • G. Allan Johnson– Duke University, North Carolina, USA

  • David Leopold –National Institute of Mental Health; NIHNeurophysiology Imaging Facility, Maryland, USA

  • Henry Markram– Brain Mind Institute; theBlue Brain Project; Swiss Federal Institute for Technology (EPFL), Lausanne, Switzerland

  • Troy Margrie– MRC National Research Institute of Medical Research, London, UK

  • ParthaMitra– Cold Spring Harbour Laboratory, New York, USA

  • Tony Movshon– New York University, New York, USA

  • Keiji Tanaka– RIKEN Brain Sciences Institute, Wako, Japan

  • Jonathan Victor– Weill Cornell Medical College, New York, USA

Associate Investigators (AIs)

  • Derek Arnold – University of Queensland, Brisbane, QLD

  • Sofia Bakola – Monash University, Melbourne, VIC

  • John Bekkers–Australian National University, Canberra, ACT

  • Anthony Burkitt – University of Melbourne; Bionic Vision Australia, Melbourne, VIC

  • Vincent Daria – Australian National University, Canberra, ACT

  • Paul Dux – University of Queensland, Brisbane, QLD

  • Alex Fornito – Monash University, Melbourne, VIC

  • Geoff Goodhill – University of Queensland, Brisbane, QLD

  • Ted Maddess – Australian National University, Canberra, ACT

  • FarshadMansouri – Monash University, Melbourne, VIC

  • Nicholas Price – Monash University, Melbourne, VIC

  • Fabio Ramos – University of Sydney, Sydney, NSW

  • Olaf Sporns–Indiana University, Bloomington, Indiana, USA

  • Naotsugu Tsuchiya – Monash University, Melbourne, VIC

  • TrichurVidyasagar – University of Melbourne, Melbourne, VIC

  • Charles Watson – University of New South Wales, Sydney, NSW; Curtin University, Perth, WA

Coordinators

  • Sarah Dunlop –Coordinator for Women in Neuroscience, University of Western Australia, Crawley, WA

  • Pulin Gong – Co-Coordinator for Neuroinformatics and Computer Resources, University of Sydney, Sydney, NSW

  • WojtekGoscinski – Co-Coordinator for Neuroinformatics and Computer Resources, Monash University, Melbourne, VIC

  • JakobHohwy–Coordinator for Society and Ethics, Monash University, Melbourne, VIC

  • Rachel Nowak – Director of the Brain Dialogue, Coordinator for Outreach, Monash University, Melbourne, VIC

Fellows

  • RomeshAbeysuriya –(Peter Robinson) University of Sydney, Sydney, NSW

  • Mehdi Adibi – (EhsanArabzadeh) Australian National University, Canberra, ACT

  • TaherehBabaie– (Peter Robinson) University of Sydney, Sydney, NSW

  • GurshChana – (Stan Skafidas) University of Melbourne, Melbourne, VIC

  • Shaun Cloherty – (Michael Ibbotson) University of Melbourne, Melbourne, VIC

  • Calvin Eiber – (Paul Martin) University of Sydney, Sydney, NSW

  • Yuhong Fu – (George Paxinos) University of New South Wales, Sydney, NSW

  • Leonardo Gollo – (Michael Breakspear), Queensland Institute of Medical Research, Brisbane, QLD

  • SharnaJamadar – (Gary Egan) Monash University, Melbourne, VIC

  • Tim Karle – (Steve Petrou) University of Melbourne, Melbourne, VIC

  • EhsanKheradpezhouh – (EhsanArabzadeh) Australian National University, Canberra, ACT

  • Sammy Lee–(Ulrike Grünert) University of Sydney, Sydney, NSW

  • Andy Liang– (George Paxinos) University of New South Wales, Sydney, NSW

  • PiotrMajka – (Marcello Rosa) Monash University, Melbourne, VIC

  • Roger Marek – (PankajSah) University of Queensland, Brisbane, QLD

  • Hamish Meffin – (Michael Ibbotson) University of Melbourne, Melbourne, VIC

  • Anand Mohan – (Arthur Lowery) Monash University, Melbourne, VIC

  • Babak Nasr – (Stan Skafidas) University of Melbourne, Melbourne, VIC

  • Bryan Paton – (Gary Egan) Monash University, Melbourne, VIC

  • Sander Pietersen – (Paul Martin) University of Sydney, Sydney, NSW

  • SivaramanPurushothuman – (Ulrike Grünert) University of Sydney, Sydney, NSW

  • Emma Schofield – (George Paxinos) University of New South Wales, Sydney, NSW

  • Guilherme Silva – (Greg Stuart) Australian National University, Canberra, ACT

  • Dongping Yang – (Peter Robinson) University of Sydney, Sydney, NSW

Scholars

  • Natasha Gabay –(Peter Robinson) University of Sydney, Sydney, NSW

  • Adam Keane – (Peter Robinson) University of Sydney, Sydney, NSW

  • Xiaochen Liu– (Peter Robinson) University of Sydney, Sydney, NSW

  • Jessica McFadyen – (Marta Garrido) University of Queensland, Brisbane, QLD

  • John Palmer – (Peter Robinson) University of Sydney, Sydney, NSW

  • Mihn-Son To – (Greg Stuart) Australian National University, Canberra, ACT

  • Rory Townsend – (Peter Robinson) University of Sydney, Sydney, NSW

  • GuYifan – (Peter Robinson) University of Sydney, Sydney, NSW

  • Natalie Zeater – (Paul Martin) University of Sydney, Sydney, NSW

  • Iris Zhu – (Marcello Rosa) Monash University, Melbourne, VIC

Management & Node Administrators

  • Lisa Hutton – Centre Manager, Monash University, Melbourne, VIC
  • Jessica Despard –Monash University, Melbourne, VIC

  • Cill Gross – University of Melbourne, Melbourne, VIC

  • Cindy Guy – University of Sydney, Sydney, NSW

  • Roxanne Jemison –University of Queensland, Brisbane, QLD

  • Vicki McAuliffe – Monash University, Melbourne, VIC

  • Elizabeth Paton – Monash University, Melbourne, VIC

  • Emma Schofield – University of New South Wales, Sydney, NSW

  • Danielle Ursino– Australian National University, Canberra, ACT

Advisory Board

  • Lyn Beazley AO – Chair,(Immediate past Chief Scientist of Western Australia)

  • Amanda Caples – Government and bio-industry advisory member, (Deputy Secretary Innovation & Technology at Department of Economic Development, Jobs, Transport and Resources, State Government Victoria)

  • Ulf Eysel – International scientific advisory member, (Department of Neurophysiology, Ruhr University, Bochum, Germany)

  • Allan Jones – International neurotechnology and scientific advisory member, (CEO, Allen Institute for Brain Science, Seattle, USA)

  • John Funder–National scientific advisory member, (Honorary Fellow, Hudson Institute of Medical Research, Melbourne)

  • David Van Essen – International scientific advisory member, (Director, The Human Connectome Project, Washington University, St Louis, USA)

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ARC CENTRE OF EXCELLENCE FOR INTEGRATIVE BRAIN FUNCTION Personnel

Centre Contributors - Fellows

  • Ben Allitt –(Marcello Rosa) Monash University, Melbourne, VIC

  • DuwageAlwis – (Marcello Rosa) Monash University, Melbourne, VIC

  • Kevin Aquino– (Peter Robinson) University of Sydney, Sydney, NSW

  • EleonoraAutuori – (PankajSah) University of Queensland, Brisbane, QLD

  • Corinne Bareham – (Jason Mattingley) University of Queensland, Brisbane, QLD

  • Oliver Baumann – (Jason Mattingley) University of Queensland, Brisbane, QLD

  • KonstantinosChatzidimitrakis – (Marcello Rosa) Monash University, Melbourne, VIC

  • Luca Cocchi – (Jason Mattingley) University of Queensland, Brisbane, QLD

  • Bill Connelly (Greg Stuart) Australian National University, Canberra, ACT

  • Christine Dixon – (PankajSah) University of Queensland, Brisbane, QLD

  • Hannah Filmer – (Jason Mattingley) University of Queensland, Brisbane, QLD

  • Maureen Hagan–(Marcello Rosa) Monash University, Melbourne, VIC

  • Kaori Ikeda– (Greg Stuart) Australian National University, Canberra, ACT

  • Marc Kamke – (Jason Mattingley) University of Queensland, Brisbane, QLD

  • Cliff Kerr – (Peter Robinson) University of Sydney, Sydney, NSW

  • Delphine Levy-Bencheton – (Jason Mattingley) University of Queensland, Brisbane, QLD

  • James MacLaurin – (Peter Robinson) University of Sydney, Sydney, NSW

  • Natasha Matthews – (Jason Mattingley) University of Queensland, Brisbane, QLD

  • Adam Morris – (Marcello Rosa) Monash University, Melbourne, VIC

  • John Morris – (PankajSah) University of Queensland, Brisbane, QLD

  • Christopher Nolan – (PankajSah) University of Queensland, Brisbane, QLD

  • David Painter – (Jason Mattingley) University of Queensland, Brisbane, QLD

  • Svetlana Postnova– (Peter Robinson) University of Sydney, Sydney, NSW

  • ParneshRaniga –(Gary Egan) Monash University, Melbourne, VIC

  • Margreet Ridder – (PankajSah) University of Queensland, Brisbane, QLD

  • SusmitaSaha – (Michael Ibbostson) University of Melbourne, Melbourne, VIC

  • Martin Sale – (Jason Mattingley) University of Queensland, Brisbane, QLD

  • Paula Sanz-Leon – (Peter Robinson) University of Sydney, Sydney, NSW

  • SomwritaSarkar – (Peter Robinson) University of Sydney, Sydney, NSW

  • Peter Stratton – (PankajSah) University of Queensland, Brisbane, QLD

  • Cornelia Strobel – (PankajSah) University of Queensland, Brisbane, QLD

  • Robert Sullivan – (PankajSah) University of Queensland, Brisbane, QLD

  • Fabrice Turpin – (PankajSah) University of Queensland, Brisbane, QLD

  • AshikaVeghese– (Jason Mattingley) University of Queensland, Brisbane, QLD

  • Francois Windels – (PankajSah) University of Queensland, Brisbane, QLD

  • Hsin-Hao Yu –(Marcello Rosa) Monash University, Melbourne, VIC

  • Elizabeth Zavitz –(Marcello Rosa) Monash University, Melbourne, VIC

Centre Contributors - Scholars