Thesis by publication and candidature management

Thesis by Publication
Workshop and QA Session
Dr Jennifer Rowland
Science, Engineering, and Medicine
Learning Skills Advisor
Dean HDR Office

• Candidate management plan
• University guidelines for thesis by publication
• Individual sections of the thesis
• Further help and support
• Open the floor to further discussion
* Questions permitted throughout *
Workshop and QA Session

http://www.mq.edu.au/policy/docs/hdr_thesis/guideline_by_publication.html
PhD Candidates
Candidature Management Plan
• http://www.hdr.mq.edu.au/information_for/ne
w_candidates/cmp
• 3 year candidature management plan
• In consultation between candidate and
supervisor
o Definition of milestones
o Thesis/publishing plan
o Timeline and deliverables

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 31 32 33 34 35 36
SET
UP
GENERATE CONTENT
COMPLETE
• http://www.hdr.mq.edu.au/information_for/new_candidates/cmp

NO LEAVE
1 2 3 4 5 6
Orientation
Attend Commencement Programs
Research Proposal and timeline
Research Proposal confirmed
Ethics applications
Commencement Report
Candidature Management PlanSETUP
Formal Faculty Review
Candidature Confirmation
Publication and Financial plan finalised
Research design & methodology done
Ethics approved
Thesis completion timetable set
Check HDRO Res Student Profile details
Data collection commences

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
Thesis completion timetable revised
Data collection
Annual Report/MUSEQ-R
PGRF applications
Data Analysis
Literature Review (complete/revised) C R
Chapters (draft/final) D D D D D D D F F F F F F
Examiner selection
Presubmission review (faculty)
GENERATE CONTENT

COMPLETE
30 31 32 33 34 35 36
Chapters (draft/final)
F
Examiner selection
Completion report (faculty)
Thesis submission

NO LEAVE
Orientation
Attend Commencement Programs
Research Proposal and timeline
Research Proposal confirmed
Ethics applications
Commencement Report
Formal Faculty Review
Candidature Confirmation
Publication and Financial plan finalised
Research design & methodology done
Ethics approved
Thesis completion timetable
Annual Report/MUSEQ-R
Data collection
PGRF applications
Data collection
Data Analysis
Literature Review (complete/revised) C R
Chapters (draft/final) D D D D D D D F F F F F F
Examiner selection
Completion report (faculty)
Thesis submission

A thesis by publication may include relevant papers, including
conference presentations, which have been published, accepted,
submitted or prepared for publication for which at least half of
the research has been undertaken during enrolment.
Thesis by publication may be a better fit with disciplines where
a research question is answered by work in discrete stages or
involves a sequence of related components (e.g., a series of
laboratory experiments or production of creative works).
AP Judi Homewood, AD HDR, FHS
A thesis by publication may include relevant papers, including
conference presentations, which have been published,
accepted, submitted or prepared for publication for which
at least half of the research has been undertaken during
enrolment.
Thesis by publication may be a better fit with disciplines where
a research question is answered by work in discrete stages
or involves a sequence of related components (e.g., a series
of laboratory experiments or production of creative works).
AP Judi Homewood, AD HDR, FHS

• relevant papers/conference presentations
• published, accepted, submitted or prepared
• at least half performed during enrolment
• research question is answered
• stages/sequence of related components

• No reformat of papers needed
• Simple binding together not enough
• Include
• a Critical Introduction to the work
• Sections that LINK the papers together, and
• Concluding Section for material as a whole
OVERALL COHERENCE
HOW EACH PAPER CONTRIBUTES

• 2 – 8 papers
sole and joint authorship
• Each paper a thesis chapter
• Not necessarily chronological
• Clear coherent research study presentation
• Maximum 100,000 words
• Under clear authorship protocols
Present with the Code for Responsible Conduct of Research in mind
http://www.mq.edu.au/__data/assets/pdf_file/0019/71065/The20Macquarie20University20Co
de20for20the20Responsible20Conduct20of20Research.pdf

Paper 1 Paper 2 Paper 3 Paper 4

Paper 1 Paper 2 Paper 3 Paper 4
INTRODUCTION
CONCLUSIONS
BIBLIOGRAPHY/REFERENCES
TITLE PAGE
STATEMENT OF ORIGINALITY
ABSTRACT/SUMMARY
ACKNOWLEDGEMENTS
TABLE OF CONTENTS
LIST OF CONTRIBUTORS/CONTRIBUTIONS
LIST OF ORIGINAL PUBLICATIONS
AIMS OF STUDY
ABBREVIATIONS
APPENDICES

• Permission to publish your papers in your thesis
• Format for the manuscript
• Style of writing for joint author papers will
differ from the other thesis sections
o Active or passive language
o Referencing will be central
o Encompasses whole thesis

Thesis Format – PhD, MPhil and MRes
http://www.hdr.mq.edu.au/information_for/current_candidates/thesis_preparation#presentation
cv cv
Double or 1.5
spaced text Double-sided
printing
Medium-weight
paper
High-quality
printing (laser)
BINDINGEDGE
3.5cm margin
on binding
edge 1.5cm margin
cv
cv 1.5cm margin

TITLE PAGE
• Title of the thesis in full
• Names and degrees of the candidate
• Name of the organisation, institute or laboratory in
which the research was carried out (if applicable)
• Name of the host University Department
• Date when submitted or re-submitted for the degree
• Statement of presentation

cv cv
cv
cv
Intracellular Signalling of IGFI
Jennifer Rowland
BSc. M.Res
Department of Biological Sciences
Faculty of Science and Engineering
Macquarie University
NSW Australia
Presented for the degree of
Doctor of Philosophy
On
February 18, 2016

Investigation of the Properties of
Adipose-Derived Cells and Secretions
Sinead Blaber
Bachelor of Biotechnology (Honours)
University of Technology, Sydney
A thesis submitted in partial fulfilment of the requirements for the degree of
Doctor of Philosophy
Department of Chemistry and Biomolecular Sciences,
Macquarie University
Sydney, Australia
Submitted for examination: November 2012
Final Submission: August 2013

This thesis is the result of my own work and
includes nothing which is the outcome of work
done in collaboration except where specifically
indicated in the text. This work has not been
submitted for a higher degree to any other
university or institution.
Jennifer Rowland

DECLARATION
I certify that the work in this thesis entitled “Investigation of the
Properties of Adipose-Derived Cells and Secretions” has not
previously been submitted for a degree nor has it been submitted as
part of requirements for a degree to any other university or
institution other than Macquarie University. I also certify that the
thesis is an original piece of research and it has been written by me.
Any help and assistance that I have received in my research work
and the preparation of the thesis itself have been appropriately
acknowledged.
In addition, I certify that all information sources and literature used
are indicated in the thesis.
The research presented in this thesis was approved by the
Macquarie University Human Research Ethics Committee,
reference number:
Human Ethics Approval:
5201100385 – 2011
Biosafety Approval
5201000874 – 2010
Some of the research presented in this thesis (Chapter 4) was
approved by the University of Queensland’s Animal Ethics
Committee. Confirmation of this approval was provided to the
Macquarie University Animal Ethics Committee.
Animal Ethics Approval:
TETRAQ/331/11/REGENEUS – 2011
Sinead Blaber (4217 4686)
30th November, 2012

• Work not submitted elsewhere for a higher
degree
• Indicate that sources of information referenced
• Outline Ethics clearances
http://www.hdr.mq.edu.au/information_for/thesis_examiners/documents/HDR_Thesis_Preparation_Advice_Aug_08.pdf

TABLE OF CONTENTS
• Use a document map/headings to make your table of
contents
• You might want to use Captions to create a separate
table of contents for tables and figures
• Prepages page numbered i, ii, iii, iv…
• Pages numbered 1, 2, 3, 4…
• Sections Numbered 1, 1.1, 1.1.1, 2, 2.1, 2.1.1, 3…
• Paper Numbers I, II, III, IV……

TABLE OF CONTENTS
• May be followed by or associated with:
•List of Tables
•Table 1.1
•Table 1.2 ….
•List of Figures
•Figure 1.1
•Figure 1.2
•Figure 2.1 ….

This thesis is based on the following original publications,
which are referred to in the text by Roman numbers.
Original publications are reproduced with permission from
their copyright holders.
I Kuja-Panula J*, Kitomäki M*, Yamashiro T, Rouhiainen A,
Rauvala H (2003) AMIGO, a transmembrane protein in axon
tract development, defines a novel protein family with leucine-
rich repeats. Journal of Cell Biology 160(6): 963-973. doi:
10.1083/jcb.200209074a
II Kitomäki M, Jones J, Smith MM, Rauvala H (2005) AMIGO
in oncogenesis. Nature Cell Biology 290(8):34-42. doi:
19.1029/ncb.200308123a
* Equal contributors

III Kitomäki M, Smart J, Rouhiainen A, Rauvala H (2003)The
role of AMIGO, in neural development in utero.
Submitted to Development.
IV Kitomäki M, Jones J, Smith MM, Rauvala H (2005) AMIGO
in injury repair. Cell, in press.
V Kitomäki M*, Jones J*, Smith MM, Rauvala H (2005) Binding
characteristics of AMIGO: designing therapeutics for burn
therapy. Burns, accepted.
* Equal contributors

LIST OF CONTRIBUTORS
• Papers are single- or co-authored.
• Candidate must specify his/her specific contribution.
• The contribution of others to the preparation of the thesis or
to individual parts of the thesis should be specified
o Acknowledgments
o Footnotes/Endnotes
o List of contributors
• Candidate would usually be principal author
o evidence of this should appear in the appropriate
manner for the discipline.
• Examiners assess quality & extent of candidate’s contribution

Supervisor Professor Jona Jonasson
Department of Computing
Macquarie University, Australia
Associate Supervisor Associate Professor Dick Wilkins
Waikato Institute of Technology
University of Waikato, New Zealand
Internal Examiner Professor Rob Jones
Maths Hub
Macquarie University, Australia
External Examiner Doctor Tim Robbins
Department of Engineering
Helsinki University, Finland

Author’s Contribution:
I: In paper I, I performed the cloning experiments to create
the DNA constructs required for the synthetic proteins
and bioactivity assays. I performed all transfection and
transformation experiments, and together with DJW did
fermentation experiments, ion-exchange chromatography,
and crystallization for pure protein extracts. The work was
performed under the supervision of Prof Robert Jones with
the guidance of Dr Geoffrey Smith.
Your contribution specified

Author’s Contribution:
I: In paper I, all experimental procedures and paper
preparation were performed by myself, JER, with the
exception of the following: 1) Protein expression and
crystallization was done together with DJW; 2) Cell culture
was assisted by TAM; 3) Paper revisions were made by all
contributing authors, under the mentorship of RBJ and
GNS.
* Authors are referred to by their initials, full details in the original article.
Others’ contributions specified

I II III IV V
Conception &
design
DD, MR, NL MR, DD NL, DD DD, MR, DD, MR, MW
Planning &
implementation
DD DD, MR NL, DD, DD, MR, MW DD, MW
Data collection DD, NL DD NL, DD MW, DC, DD DD
Analysis &
interpretation
DD, DD, MR, NL DD, MW, DD, DC, MW, MW, DD,
Writing the article
DD, AT, MR,
NL, LF DD, MR, AT DD, MW, AT,
MR
DD, AT, MW,
MR
MW, DD, AT,
MR
Overall
responsibility
DD DD DD DD MW
DIVISION OF LABOUR IN CO-AUTHORED ARTICLES
AT - Alana Top; DC - Dale Cane; DD - Dephina Dean; LF - Lucy Frond; MR - Mike Riser; MW - Michele Wing; NL - Nancy Light.

ACKNOWLEDGEMENTS
• Try to group the acknowledgements into paragraphs
“I am immensely grateful to my colleagues in the VTHRC Research
Centre, including: John for assisting with specimen collection, Anna for
helping with formatting, Joseph for securing all my bookings,…..”
• People read your acknowledgements to get a feeling
for who you are as a person, don’t overlook them
• Use exceptional language

ABSTRACT/SUMMARY
• A synopsis / abstract of the thesis
• Summarising the appropriate headings, aims, scope and
conclusion of the thesis
• approximately 300 words for a Doctorate
(Typically 1-2 pages)

ABSTRACT/SUMMARY
• Consider breaking it up into the following sections
1: Introduction of field
2: Identification of gap in field
3: Contribution of each paper in sequence
(refer to by roman numeral, I, II, III….)
4: How the body of work has contributed to
bridging the gap in knowledge

cv cv
cv
cv
Abstract
INTRO
GAP
I
II
III
IV
CONCLUSION

INTRODUCTION
• Ties all the sections together
• May have tables or figures that demonstrate concepts
o ones you have made
o from articles *referenced*
o modified from articles *referenced*
• More expansive than the introduction that might be in a
paper
• History leading to the current study
• Overview of current State of the Art
• Relevance of the current study
• Should naturally lead to the next section where you state the
overall aims of this thesis work

INTRODUCTION
Example Figure from Introduction
http://hdl.handle.net/1959.14/305872
Appetite and
Energy Balance Blood pressure
regulation
Angiogenesis
HemostasisInflammation,
Immunity and acute
phase response
Insulin
sensitivity
Lipid
Metabolism
Figure 1.1 Diverse role of adipose tissue.
Figure adapted from (6).

Figure 1. Position of individual articles I-V within different thematic areas.
Protein
Synthesis
Binding and
Signalling
in vitro
Computational
Modelling
Delivery and Device
Development
Article II
Modelling of
Binding Interactions
of lead molecule
with target receptor
Article I
Developing a
model of lead
molecule and its
synthesis
Article IV
Development of
device for
therapeutic
delivery
Article III
Binding,
Bioactivity and
signalling
efficacy of lead
molecule
INTRODUCTION
Example Figure
from
Introduction

Table 2. Statistics of water resources in Australia (FRU, 2016)
1990 2010 2016
Annual Change
Rate
1990-2016
Dammed water Man made na na 2000 na
(42%)
Naturally occurring na na 3200 na
(58%)
Reservoirs Public 4200 3800 na na
Private 5000 5600 na na
Usage rights (all) Public 8000 7200 6000 15%
Private 1000 3000 5000 500%
Home tank users 800 14000 45000 500%
INTRODUCTION
Example Table from Introduction

AIMS OF THE STUDY
• Simple one-page summary outlining the main aims
of the study overall
• Reflects the main foci of your articles
• You can reference the articles in roman numerals
Given the importance of what you have presented that needs to be addressed in the
introduction, this thesis will address on the following research foci:
I) To determine the manner in which…. through X approach
II) To assess the essential pathway necessary for XXX via the YYY method.
III)……
IV)……
These individual investigations will be presented here referred to by their respective
roman numeral.

METHODS
• Overview of the methods in the whole study
• Perhaps include more detail on specific approaches taken
• Clarify the types of approaches taken throughout the study
The four articles in this thesis mainly employed quantitive analysis of
gene expression and/or cell-analysis research methods (Table 2).
Article I employs …..
Article II utilizes…..

METHODS
Table 2. Methods and data employed in the articles.
Article Analysis Data
I Part 1: Literature review
Part 2: Gap analysis of existing
and required water sources in
the entire Australian continent,
with reference to current
services and suppliers.
Part 1: Peer-reviewed articles and grey literature on issues
related to water resources and dependencies on different
sources throughout Australia between 2001 and 2014
(n=46).
Part 2: The Australian Water Board and services
classification and record of national water supply
provided by the Federal WB report released in 2015.
II Regional mapping GIS data generated from Murray-Darling river basin.
Sourced from state survey published in 2015.a
III Qualitative review Perspectives of state water boards and commercial
suppliers (n=50). Data collected through interview-
delivered questionnaires during June-December 2015).
IV Descriptive statistics and
qualitative content analysis.
Perspectives of local households gathers through open-
and close- ended (n=100). Data collected through
interview-delivered questionnaires during December
2015 in the Murray-Darling river basin.

STUDY CHAPTERS - PAPERS
• Each chapter/paper has an
introductory page/section
• Each introductory page sets the scene introducing the
paper and how it fits into the overall study
Article I
This paper is based on an analysis of ….
Article II
Based on the outcomes of Article I, the next natural
step to drive the work forward was to address …..

STUDY CHAPTERS - PAPERS
• The chapter may be a journal article or
conference proceeding
• It should be published in its original
format
• Permission to publish it in your thesis must be obtained
from the journal where it has been published already
(once it is published the journal owns the material)
• Each article should be able to stand alone
• They should be arranged in a logical flow of ideas, not
necessarily chronological

CONCLUSIONS
• Ties together all of the study findings
• Should be discussed in the same order as the papers
presented
• Refer to the papers by roman numerals (I, I, III…)
• Outline the overall major contributions to the field
• Outline the shortfalls and work that might be pursued
further, FUTURE DIRECTIONS
• Employ figures/diagrams to clarify outcomes where
appropriate

APPENDICES
• Questionnaires – in full
• Technical details of the work/analysis
• Survey Outlines
• Ethics Approvals
• Safety Approvals
• Supplementary Material
• NCBI published sequences
• Extra articles/papers that may be relevant to the
overall thesis

• Look at example theses in your field
• Come and see your Learning Advisor
• Attend WriteNow! Sessions
(Wednesdays, W6B 357, 12-2PM)
• Make sure that you keep an up to date schedule of your
thesis plan (CMP)
• Stay focused on your overall goal, don’t get side-tracked
with peripheral tasks
• Have regular project meetings with your supervisor/mentor
• Start writing as early as possible
Final Thoughts

Want more help?
Check out the writing courses on the HDR workshops page
https://hdrworkshops.mq.edu.au/
Basic Writing
Writing for Publication
Writing a Literature Review
Endnote Courses
Statistics Courses
Thesis Formatting Courses
Survey Design and Data Analysis
and more…

Want more help?
Schedule an appointment with your
Dean HDR Learning Skills Advisor
Humanities
Dr Michelle Jamieson - michelle.jamieson@mq.edu.au
Social Science
Dr Florence Chiew - florence.chiew@mq.edu.au
Science, Engineering, Medicine
Dr Jennifer Rowland - jen.rowland@mq.edu.au

REFERENCE MATERIAL
• HDR OFFICE – HDR Thesis Preparation Advice
http://www.hdr.mq.edu.au/information_for/thesis_examiners/documents/
HDR_Thesis_Preparation_Advice_Aug_08.pdf
• Code for Responsible Conduct of Research
http://www.mq.edu.au/__data/assets/pdf_file/0019/71065/The20Macquari
e20University20Code20for20the20Responsible20Conduct20of20Research.pdf
• Thesis by Publication Guideline
http://www.mq.edu.au/policy/docs/hdr_thesis/guideline_by_publication.ht
ml

Printing
• For students who wish to organise their own printing and
binding we have been using Allbook Bindery at West Ryde
for many years now for the hardcase binding, and they will
also be able to do the printing. Their quality craftsmanship
and service is to be highly recommended.
•
• Quotes and orders can be placed online via:
•
• http://allbookbindery.com/
•
• Contact number is 9807 6026
• Email: contact@allbook

Thesis by publication and candidature management

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