Thesis by publication and candidature management

Thesis by Publication Workshop and QA Session

Dr Jennifer RowlandScience, Engineering, and Medicine

Learning Skills AdvisorDean 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 *

Thesis by Publication 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 milestoneso Thesis/publishing plano Timeline and deliverables

http://www.hdr.mq.edu.au/information_for/new_candidates/cmp

Candidature Management Plan1 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

CO

MP

LETE

• 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 PlanSE

T U

P


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 CONTENTCandidature Management Plan


Candidature Management Plan

CO

MP

LETE

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

Candidature Management Plan

Thesis by Publication

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 paperssole and joint authorship

• Each paper a thesis chapter

• Not necessarily chronological

• Clear coherent research study presentation

• Maximum 100,000 words

• Under clear authorship protocolsPresent with the Code for Responsible Conduct of Research in mind

http://www.mq.edu.au/__data/assets/pdf_file/0019/71065/The20Macquarie20University20Code20for20the20Responsible20Conduct20of20Research.pdf


Paper 1 Paper 2 Paper 3 Paper 4



Paper 1 Paper 2 Paper 3 Paper 4

INTRODUCTION

CONCLUSIONSBIBLIOGRAPHY/REFERENCES

TITLE PAGESTATEMENT OF ORIGINALITY

ABSTRACT/SUMMARY

ACKNOWLEDGEMENTS

TABLE OF CONTENTS

LIST OF CONTRIBUTORS/CONTRIBUTIONSLIST 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 languageo Referencing will be centralo 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)

BIN

DIN

G E

DG

E

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

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Intracellular Signalling of IGFI

Jennifer RowlandBSc. M.Res

Department of Biological SciencesFaculty of Science and Engineering

Macquarie UniversityNSW Australia

Presented for the degree ofDoctor of Philosophy

OnFebruary 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

STATEMENT OF ORIGINALITY

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

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

STATEMENT OF ORIGINALITY

• 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 ….

LIST OF ORIGINAL PUBLICATIONS

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

LIST OF ORIGINAL PUBLICATIONS

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 JonassonDepartment of ComputingMacquarie University, Australia

Associate Supervisor Associate Professor Dick WilkinsWaikato Institute of TechnologyUniversity of Waikato, New Zealand

Internal Examiner Professor Rob JonesMaths HubMacquarie University, Australia

External Examiner Doctor Tim RobbinsDepartment of EngineeringHelsinki 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 articleDD, 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

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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…

https://hdrworkshops.mq.edu.au/

Want more help?

Schedule an appointment with your

Dean HDR Learning Skills Advisor

Humanities

Dr Michelle Jamieson - [email protected]

Social Science

Dr Florence Chiew - [email protected]

Science, Engineering, Medicine

Dr Jennifer Rowland - [email protected]

mailto:[email protected]



REFERENCE MATERIAL

• HDR OFFICE – HDR Thesis Preparation Advice


• Code for Responsible Conduct of Research


• Thesis by Publication Guideline





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

http://allbookbindery.com/

Education

Thesis by publication and candidature management