JRowland_thesis_Flinders

INCLUDING PUBLICATIONS IN
YOUR THESIS
Dr Jennifer Rowland
Director of Master of Research Program
Faculty of Medicine and Health Sciences
Macquarie University

2
• Guidelines for including publications in thesis
• Individual sections of the thesis
• Professional Editing
Including Publications in your Thesis

• 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 Academic Integrity Policy in mind
http://www.flinders.edu.au/ppmanual/student/academic-integrity.cfm
Thesis by Publication

Paper 1 Paper 2 Paper 3 Paper 4
Thesis by Publication

• Book chapters
• Conference proceedings
• Journal articles (online and print)
• Prepared manuscripts

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

Including Publications in Thesis
• 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

https://www.flinders.edu.au/content/dam/documents/staff/policies/academic-students/hdr-thesis-rules.pdf

Thesis Format – PhD, MPhil, and MRes
cv cv
Double or 1.5
spaced text
BINDINGEDGE
3.5cm margin
on binding
edge 1.5cm margin
cv
cv 1.5cm marginHigh-standard of
presentation
Font 11-12pt
http://www.hdr.mq.edu.au/information_for/current_candidates/thesis_preparation#presentation

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
1.5cm margin
1.5cm margin
cv
cv 1.5cm marginHigh-standard of
presentation
Font 11-12pt
Margins moderate
(discipline appropriate)

TITLE PAGE
• Title of the thesis in full
• Names and degrees of the candidate
• Name of the College most associated with the work
• Date when submitted/re-submitted for the degree

cv cv
cv
cv
Intracellular Signalling of IGFI
Jennifer Rowland
BSc. M.Res
Department of Biological Sciences
Faculty of Science and Engineering
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,
Sydney, Australia
Submitted for examination: November 2012
Final Submission: August 2013

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 ….
Use captions if you’re
using Microsoft Word

DECLARATION
• Signed by student
• Work not submitted elsewhere for a
degree/diploma
• Indicate that sources of information referenced
• *Outline Ethics clearances
*Common practice

DECLARATION
“I certify that this thesis does not incorporate without
acknowledgment any material previously submitted for a degree
or diploma in any university.
To the best of my knowledge and belief, this thesis does not
contain any material previously published or written by another
person except where due reference is made in the text.
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

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
Acknowledgment by the student of help given or work carried out by
another person or organisation
Recipients of RTP support (fees offsets, stipends or allowances) must
acknowledge the contribution of an
“Australian Government Research Training Program Scholarship”
in the thesis and in any publications that arise directly from the
research undertaken during the candidature.

• 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
• No more than 500 words
(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 study chapter/paper in sequence
(refer to by roman numeral, I, II, III…., or Arabic numeral 1, 2, 3…)
4: How the body of work 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.

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:
Chapter 3 To determine the manner in which…. through X approach (Paper I)
Chapter 4 To assess the essential pathway necessary for XXX via the YYY method
(unpublished)
Chapter 5 …… (Paper II)
Chapter 6 …… (Paper III)
These individual investigations will be presented here referred to by their respective
roman numeral or Chapter number.

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
• % Contribution clarified in prose
• 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 other
peer-reviewed content
(conference proceeding, book chapter,…)
• Published in its original format?
• Accepted, submitted, or in manuscript form*
• 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
REFORMATTED TO
THESIS STYLE

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…)
• Refer to results chapters with Arabic numbers (1, 2, 3…)
• 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

BIBLIOGRAPHY
INTRODUCTION
TITLE PAGE
DECLARATION
ABSTRACT/SUMMARY
ACKNOWLEDGEMENTS
TABLE OF CONTENTS
AIMS OF STUDY
ABBREVIATIONS
CONCLUSIONS
APPENDICES
I II III IV
INTRODUCTION
TITLE PAGE
DECLARATION
ABSTRACT/SUMMARY
ACKNOWLEDGEMENTS
TABLE OF CONTENTS
AIMS OF STUDY
ABBREVIATIONS
CONCLUSIONS
APPENDICES
I II III IV
METHODS
RESULTS/GENERAL
INTRODUCTION
TITLE PAGE
DECLARATION
ABSTRACT/SUMMARY
ACKNOWLEDGEMENTS
TABLE OF CONTENTS
AIMS OF STUDY
ABBREVIATIONS
CONCLUSIONS
APPENDICES
METHOD/SUMMARY
RESULTS CHAPTER I
RESULTS CHAPTER III
RESULTS CHAPTER II
RESULTS CHAPTER IV

INTRODUCTION
TITLE PAGE
DECLARATION
ABSTRACT/SUMMARY
ACKNOWLEDGEMENTS
TABLE OF CONTENTS
AIMS OF STUDY
ABBREVIATIONS
CONCLUSIONS
APPENDICES
METHOD/SUMMARY
RESULTS CHAPTER I
RESULTS CHAPTER III
RESULTS CHAPTER II
RESULTS CHAPTER IV
• Doesn’t change due date
• References central for all chapters
• Results all presented in “thesis style/format”
• Clarity re: published and unpublished content
• Low repetition for introduction and conclusions
• May include papers in published format in appendices
The Flinders Thesis
including publications

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
• Papers where you are not the primary author

• Find exemplars in your field
• Refer to Learning Advisors and Research Librarians
• Promote regular writing practice
• Make sure that you keep an up-to-date schedule of the
thesis plan
• Keep focused on research goals
• Have regular project meetings
• Start writing/planning as early as possible
Final Thoughts

How can a professional editor help you?
http://iped-editors.org/About_editing/Editing_theses/FAQ_editors.aspx
https://www.flinders.edu.au/graduate-research/examination-and-completion/preparing-a-
thesis-for-examination/having-your-thesis-edited.cfm
Professional editing of a thesis refers to editing services which are paid for.
1. Professional editing must be undertaken before the final version of the thesis is
submitted to the student's supervisor for consideration.
2. Supervisors must oversee the process and monitor professional editing on an individual
basis.
3. Professional editing must be limited to formatting, grammar
and style and must not alter or improve the substantive content
or conceptual organisation of the thesis.
4. Candidates should include an acknowledgement of the help
given or work carried out by another person or organisation in
editing their thesis.

Ensure correct
• spelling
• grammar
• punctuation
• make text clear and natural sounding
• clarify ambiguities
• address text inconsistencies
Language revision does not involve or correct the following
1) Structure of the text
•For example, order of paragraphs
2) Content issues, such as faulty or unclear argumentation
•Your revisor may, however, offer advice on or attempt to
resolve obvious problems.
3) Citations and references
UK/US?
Subject/verb, syntax, articles, prepositions, tenses, grammar
periods, colons, semi-colons, commas, etc.
voice and style, sentence cohesion,
consistent vocabulary and terminology
https://www.helsinki.fi/en/language-centre/cooperation-and-language-services/language-
revision-services-at-the-university-of-helsinki

Services editors may provide in editing research theses are limited
to copyediting and proofreading
Australian standards for editing practice
Must check with students whether their institution requires editing in hard
copy or will allow theses to be edited onscreen.
Students should obtain permission from their principal supervisor before
engaging an editor - evidence of that permission.
Some practical concerns
Editor should be acknowledged in the prefatory matter to
the thesis. The acknowledgement could take the following
form:
‘Professional editor, [editor’s name], provided copyediting
and proofreading services, according to the guidelines laid
out in the university-endorsed national ‘Guidelines for
editing research theses’.

Some practical concerns
Provide
• clean copy of thesis.
• any style guide, manual or other guidelines
Clarify
• students’ role during the editing process.
• students are responsible for the final product
o editorial suggestions
o checking changes individually
Alert
• regarding problems in matters of substance or structure
• provide examples to guide in resolving these
• unethical practices (sometimes with supervisor)
http://iped-editors.org/Find_an_editor.aspx

THESIS BY PUBLICATION
Dr Jennifer Rowland
Director of Master of Research Program
Faculty of Medicine and Health Sciences
www.practicalacademic.com

REFERENCE MATERIAL
• HDR OFFICE – HDR Thesis Preparation Advice
http://www.hdr.mq.edu.au/information_for/thesis_examiners/documents/HDR_Thesis_Preparation_Advic
e_Aug_08.pdf
• Code for Responsible Conduct of Research
http://www.mq.edu.au/__data/assets/pdf_file/0019/71065/The20Macquarie20University20Code20for20the
20Responsible20Conduct20of20Research.pdf
• Thesis by Publication Guideline
http://www.mq.edu.au/policy/docs/hdr_thesis/guideline_by_publication.html
• Flinders Thesis Rules

JRowland_thesis_Flinders

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