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Gudelines for the preparation of a Ph.D. thesis
The following pages are a guide to Ph.D. students to prepare and submit a thesis.
The student is recommended to consult their University guidelines applicable to the year in which they are submitting their thesis

PREPARATION OF A Ph.D. THESIS
by Matthew T. Gillespie
Submitted in total fulfilment of the requirements of the degree of Doctor of Philosophy
Department of Medicine
St. Vincent's Hospital
The University of Melbourne
June 1995


CONTENTS
ABSTRACT
DECLARATION OF AUTHENTICITY
ACKNOWLEDGEMENTS
LIST OF FIGURES
LIST OF TABLES
PUBLICATIONS ARISING FROM THIS WORK

CHAPTER 1 - INTRODUCTION
1.1 WORDS OF ADVICE
1.2 THE UNIVERSITY OF MELBOURNE'S REQUIREMENTS
CHAPTER 2 - MATERIALS AND METHODS
2.1 SPACING
CHAPTER 3 - FIGURE LEGENDS AND TABLES
CHAPTER 4 - REFERENCES

4.1 IN TEXT
4.2 IN THE BIBLIOGRAPH
CHAPTER 5 - ABBREVIATIONS
5.1 COMMON MISTAKES IN ABBREVIATIONS
5.2 COMMON MISTAKES IN THE TEXT
5.3 ABBREVIATIONS FREQUENTLY USED
CHAPTER 6 - TIMETABLE FOR Ph.D. SUBMISSION
CHAPTER 7 - THESIS SUBMISSION

7.1 NUMBER OF COPIES
7.2 SUPERVISOR'S ENDORSEMENT
CHAPTER 8 - EXAMINATION
8.1 TIME SPENT UNDER EXAMINATION
8.2 RECOMMENDATIONS OF EXAMINERS
8.3 CORRECTIONS AND AMENDMENTS TO THE THESIS
CHAPTER 9 - CONCLUSION
9.1 FINAL THOUGHTS
APPENDICES

DECLARATION OF AUTHENTICITY
You have to provide a declaration at the beginning of the thesis to the effect that the work presented within the text has been generated by you apart from where due reference has been made. An appropriate declaration is:

This thesis contains no material which has been accepted for the award of any other degree or diploma in any University, and is less than 100,000 words in length. To the best of my knowledge and belief, this thesis contains no material previously published or written by another person, except where due reference has been made.

J.A. Smith

Remember to sign the declaration prior to thesis submission.Monash University guidelines states that where "work in the thesis is based on joint research or publications, [the declaration] discloses the relative contributions of the respective authors. Where practicable, the statement should be countersigned by the other contributors".

CHAPTER 1
INTRODUCTION

All students are advised to read the conditions for the Degree of Doctor of Philosophy from the university in which they are enrolled prior to writing their thesis. These brochures contain information which is relevant to many facets of undertaking a Ph.D. including: rules, procedures, guidelines and advice. This booklet for both The University of Melbourne and Monash University was last updated in 1994.

1.1 WORDS OF ADVICE

I intend this handout to offer "words of advice" on the preparation of Ph.D. theses. Only too often have supervisors received first drafts of theses, manuscripts and other works where the submitting author has paid no (or very little) attention to the requirement for style or presentation of their work. This is particularly pertinent at the stage of thesis writing. Nothing is more frustrating to a supervisor, or anybody, who is proof-reading/criticising a thesis than to find that the work lacks fundamental "polish and presentation". On the other side of the coin is to advise the student of this, and their initial reaction is "Oh you're just being picky, there's nothing really wrong". Time initially spent on thesis layout and an eye to detail will be of great benefit both for the submission process and your long term involvement in manuscript and grant submissions. To offer a correctly laid out thesis to an individual to criticise means that an individual will focus on scientific relevance, logic and data and not punctuation and sentence construction.

I would like to draw your attention to some all too common pitfalls that can be found at some stage during the writing of every thesis.

1.2 THE UNIVERSITY OF MELBOURNE'S REQUIREMENTS

Format of the thesis (taken from the Degree of Doctor of Philosophy)

The following are obligatory:

(i) When the thesis is submitted, the candidate shall also submit a declaration from the supervisor and head of department that the thesis is ready to go forward to examination (form available from the Office of Graduate Studies).

(ii) Three copies of the thesis must be submitted. Monash University requires four copies of the thesis to be submitted. Check with your enrolled institution.

(iii) All three copies must contain (Prescription 18):

(a) an abstract of 300-500 words in English; and
(b) a declaration that the thesis is less than 100,000 words in length, exclusive of tables, maps, bibliographies, appendices and footnotes (unless special permission has been given to exceed this length);
(iv) International Standard Paper Size A4 should be used (but see ix below). Sheets should be numbered consecutively and clearly, and interpolated sheets should be marked distinctly. The typing should be double spaced or 1 1/2 spaced and may be presented on one or both sides of bond paper with a margin at least 3 centimetres wide on both sides of each sheet. Care should be taken with page numbers to allow for page trimming when the thesis is bound. Monash University recognises any of the "quarto" paper, namely, International A4, American Quarto or Imperial Quarto. Typing is preferred to be double spaced although 1 1/2 spacing is permitted. Margins should not be less than 4 cm on the binding edge and 1.5 cm on the outer edges to allow for binding and trimming.
(v) Folding diagrams or charts should be arranged so as to open to the top and right.

(vi) A candidate may not use reprints or journal articles in their published form as part of the body of the thesis. While a thesis may be published in whole or in part prior to submission, it should both in form and content be presented as a unified whole, prepared specifically for submission for examination for the degree. Any parts of the thesis which have been previously published should be indicated in the preface.

(vii) A title page must show the title of the thesis, the name of the department or faculty in which the research was carried out and the full name of the author. Candidates who have pursued a course of study by research alone shall state on the title page: "Submitted in total fulfilment of the requirements of the degree of Doctor of Philosophy". Candidates who have pursued a course of study with coursework component shall state: "Submitted in partial fulfilment of the requirements of the degree of Doctor of Philosophy (with coursework component)". Candidates who have pursued a course of study by thesis and musical composition shall state: "Submitted in partial fulfilment of the requirements of the degree of Doctor of Philosophy (by thesis and musical composition).

(viii) The name of the author, the title (abbreviated if necessary) and the year of submission must be on the spine.

(ix) All these should normally be presented in English. Should a candidate wish to present a thesis in a language other than English, application must be made at an early stage in the candidature. The Ph.D. Sub-Committee will consider such an application only if full justification is provided by the department and may then recommend to the Academic Board that the candidate be permitted to present the thesis in the relevant language. Where permission is granted, a substantial summary of the thesis in English should be bound in with the thesis.

(x) At the conclusion of the examination two copies of the thesis shall be made available to the Office of Graduate Studies in permanent binding so that they can stand on a shelf as books. One of these shall be printed on acid-free paper (suitable paper is available from the Bookroom). The words "Produced on acid-free paper" should be printed or typed on the title page of this copy. The remaining copy will be at the disposal of the candidate.

You will note that these guidelines are "fairly loose", and because not all aspects of thesis preparation are defined, omissions or inaccurate presentation of data, references, appendices, footnotes etc. frequently occur.

CHAPTER 2
MATERIALS AND METHODS

When stating a chemical you should provide the suppliers name in full eg., Tris (hydroxymethyl) aminomethane (Sigma Chemical Co. Ltd., St Louis, MO, USA). Any references to Sigma thereafter should be (Sigma Chemical Co. Ltd.).

Remember that we obtain chemicals from a number of local distributors eg., Amersham International Sydney, however it is manufactured and marketed from Amersham International, Buckinghamshire, UK.

The Materials and Methods section should be of sufficient detail to enable the examiner to determine what was actually undertaken.

2.1 Spacing

Be consistent in use of spacing when typing 15 min, 1 ul, 1 M and do not run them together as 15min, 1mg, 1ul, 1M.

CHAPTER 3
FIGURE LEGENDS AND TABLES

Diagrams and figures should be photocopied on A4 paper and bound in the appropriate place in the text. The figures are to appear as a right-hand page and the legend should appear at the bottom of the figure or on the page facing the figure. Alternatively, figures may be interspersed throughout the text, however if computer graphics are used the quality and resolution must be equal to that obtained by photographic reproduction.

Each figure legend should stand alone from the body of the text i.e., by reading the figure legend the figure should be self explanatory. The easiest (and most consistent) way to lay out figure legends is to have them all as a lefthand page i.e., opposing a figure bound on the righthand side. Do not number figure pages. In the text use the abbreviation Fig. 4.1. to denote the first figure for chapter 4 and provide in the front of the thesis a page listing the location of figures. For the layout of the figure legend use the same formula. The figure number, title (which may be presented in bold), then description.

Fig 4.1 Schematic representation of the PTHrP gene.

The coding regions and untranslated sequences are indicated by the closed and open boxes, respectively. Indicated above the map are the positions of the....

CHAPTER 4
REFERENCES

4.1 In Text

There are a number of ways to lay out references in the text, some of which are clearly wrong and others that become cumbersome to deal with. Most students should be able to use Reference Manager and this program should reduce the amount of time required.

I would recommend the following layouts since they are fairly uniform and easy to work with.

At the end of a sentence ...................as previously reported (Smith and Jones, 1970; Smith et al., 1972). Note, that following the authors name a comma should appear then year of publication, a semicolon should be between references. For more than two authors use the abbreviation et al., this should be in italics and a full stop should follow "al." since this is an abbreviation. When quoting more than one reference, references should be ordered in priority of chronology then the alphabetical listing of the authors. If one author has more than one publication in a given year the following can be adopted "Smith et al., 1981a, b, c; .........". When using this referencing system Smith et al., 1981a denotes the first cited reference of this series by the author and should be consistent throughout the thesis.

References in the text. "Smith and Jones (1970) or Smith et al. (1972) should be used. When using "et al." in the text do not include a comma after the authors name prior to the open bracket.

4.2 In the Bibliography

Book articles should be laid out according to the following recommendations. Name(s) of authors (surname and initials); title of book; edition (if relevant); place of publication; publication and year of publication. Where necessary, the relevant pages should be cited.

Sambrook, J., Fritsch, E.F. and Maniatis, T. Molecular Cloning. A laboratory Manual (2nd ed.) Cold Spring Harbor Laboratory Press, New York, 1989.

Journal articles should be laid out as follows: Name(s) of authors (surname and initials); title of article; journal name; volume number; page numbers; year of publication.

Smith, T.K. and Jones, J.M. Methods for PCR amplification of genomic material. Journal of Biological Chemistry. 20: 357-361, 1991.

Both The University of Melbourne and Monash University request references to be laid out according to the abovementioned format, although Monash University allows citations to follow the rules of citation adopted by one or other of the leading journals in the relevant field or discipline.

List authors alphabetically, then chronology and list the reference in full.

I am aware of two students that have not completed the references in full and have been requested to amend their thesis by including a full author list, title of publication and first and last page numbers. The best procedure that you can adopt is to provide all information in the first instance!

Your final check should be to ensure that all references cited in the text are included in the bibliography, that the names and dates of the citations are consistent.

CHAPTER 5
ABBREVIATIONS

The first rule is that you must be consistent with the abbreviations you use. Only too frequently are abbreviations altered between chapters due solely to the time difference in writing. I would recommend that at the stage of writing you have on a separate sheet of paper the abbreviations that you are using in the thesis and adhere to them so you are consistent throughout the body of the text.

Remember when you first use an abbreviation you should supply the unabbreviated name in full eg., sodium dodecyl sulphate (SDS). You should also provide a table as an appendix, listing abbreviations in alphabetical order.

5.1 Common mistakes in abbreviations

i.e., and eg., should be used and not ie, eg, or ie., e.g.,

Mr for relative molecular weight, the "r" should be subscript

HIV+, CD4+ both are superscript "+" signs.

Decide on whether to use aa or a.a. throughout the thesis and do not alter. Other abbreviations frequently altered throughout theses include:

kb to Kb, Kbp
min to min. or mins
kDa to K-Da, KDa
h to hr, hrs
ml to mls
Escherichia coli should be abbreviated to E. coli not E. coli or E. Coli.
Restriction enzyme names are derived from microorganisms and should therefore be in italics and enzyme numbers in roman numerals not arabic.

eg., EcoRI not EcoRI or EcoR1
watch out for BamHI not BamHI or BamH1
HindIII not HindIII or Hind3
Eco47III not Eco473
When using abbreviations for amino acids use the single letter code or the triple letter consistently, do not mix within a given sentence. In addition, if you use a consensus sequence such as "amino acid cleavage site sequence Arg-Xaa-Lys/Arg-Arg" do not use Arg-X-Lys/Arg-Arg. The correct terminology is Xaa.
Abbreviations are commonly a place where laboratory slang is introduced such as "endo H digestion", this should read "endoglycosidase H digestion", or "purified DNA was digested with" not "DNA was cut with".

5.2 Common mistakes in the text

The thesis is to be written in the "past tense" as all scientific writing is conducted. You should not include statements to you, such as "I undertook an analysis of", since the thesis is of your work. At the other extreme, avoid the use of "we".

Cross referencing in the thesis should be extensive as should referencing. Do not make unsupported claims - it is better to "over reference" than to "under reference".

Southern blotting is named after Ed Southern and therefore should have a capital "S". As a result of this, it is accepted that Northern and Western blotting also have upper case first letters.

Hyphenation A hyphen should be used in adjectival descriptions

"naturally-occurring plasmids" not
"naturally occurring plasmids"
genes vs proteins A gene should be in italics, while the protein product is not. "tax transcription was unaffected by the treatment" and "tax has been demonstrated to bind to the sequence motif"
Spelling English versus American

hybridisation or hybridization
hypercalcaemia or hypercalcemia
labelled or labeled
tumour or tumor
oestrogen or estrogen
If you adopt one spelling style be consistent for other words.
5.3Abbreviations frequently used:

1,25 (OH)2 D3 or 1,25 (OH)2 vit D3 1,25 dihydroxyvitamin D3
AMP/ADP/ATP adenosine (mono/di/tri)phosphate
bp base pairs
BSA bovine serum albumin
C-terminal carboxyl-terminal
cAMP 3'5'-cyclic adenosine monophosphate
CAT chloramphenicol acetyltransferase
cDNA complementary deoxyribonucleic acid
cpm counts per minute
CTF CCAAT transcription factor
d day(s)
dATP, dCTP, dGTP, dTTP deoxynucleotides (adenosine, cytidine, guanosine, thymidine)
DNA deoxyribonucleic acid
DNase I deoxyribonuclease I
EDTA ethylenediaminetetra acetic acid
EGF epidermal growth factor
FCS foetal calf serumvGAPDH glyceraldehyde-3-phosphate dehydrogenase
GM-CSF granulocyte macrophage-colony stimulating factor
h hour(s)vIBMX isobutyl methyl xanthinevkb kilobases
kd affinity constantvkDa kilodaltons
min minute(s)
mRNA messenger ribonucleic acid
N-terminal amino-terminalvnm nanometers
PAGE polyacrylamide gel electrophoresisvPBS phosphate buffered saline
PMA 4[[beta]]-phorbol myristate 13[[alpha]]-acetatevRIA radioimmunoassay
RNA ribonucleic acid
RNase ribonuclease
rpm revolutions per minute
SDS sodium dodecyl sulphate
sec second(s)
TCA trichloroacetic acid
TGF[[alpha]] transforming growth factor [[alpha]]
TGF[[beta]] transforming growth factor [[beta]]
TLC thin layer chromatography
TNF[[alpha]] tumour necrosis factor [[alpha]]
UV ultraviolet light
v/v volume per volume

CHAPTER 6
TIMETABLE FOR Ph.D. SUBMISSION

-4 to -3 years Enrolment and commencement of candidature. Begin literature review, material and methods and reference section of thesis.

-3 to - 2 years Confirmation of candidature. The University of Melbourne candidates are required to submit a research outline including literature review of approximately 2000 words one year after commencement of their candidature.

-12 months Final plan of thesis chapters and experiments to be completed. Post doctoral fellowships and positions will be pursued. Potential extensions of candidature and scholarships may be considered - consult with your supervisor.

-6 to -4 months The writing process will commence in earnest. During this period you will finalize all figures for your thesis.

Public presentation of research findings by seminar. The format of this is to be set by the Department, but optimally it would occur in the final six month period of the candidature.

At this stage you will be engaged in application for post-doctoral positions. You may be required to submit fellowship applications during this period and this should be taken into consideration.

-4 to -1 month Writing and re-writing work corrected by other colleagues and your supervisor.

-2 months Along with your supervisor decide on appropriate examiners. At The University of Melbourne, the candidate must provide an 80 word summary to be forwarded along with the list of potential examiners to the Office for Research. After lodgement of the 80 word summary, you will receive the "submission of PhD thesis: statement by supervisor and head of department (GS6B)" which must be signed by your principal supervisor (co-supervisor if the principal is absent) and presented to the School of Graduate Studies on submission of the three copies of the thesis. Your supervisor will receive an authorized copy of the 80 word summary from the School of Graduate Studies together with the "PhD examination nomination form (GS6A)." The GS6A form is required to be returned to the School of Graduate Studies within three weeks. The GS6A and GS6B forms are attatched in the appendix.

Day -10 to -14 You will be aware that you are nearly completed. Final corrections to be completed and the last outstanding items are to be dealt with. Check that printers and binders will be open in the next two weeks. Printers and binders frequently close during January and around Easter.

Day -6 Insertion of final amendments. Start to adjust pagination and check the table of contents.

Day -5 Final print of thesis. Print off top copy and proofread the entire thesis paying particular attention to pagination, typographicals, and inconsistencies in layout. Make sure that the table of contents is correct to the final page numbers.

Day -4 Collate all typed pages to be taken to the printer. Organize the thesis as it would be bound, but keep figure legends and tables at the back of the top copy. Ensure that the printer will print your copies on acid-free paper.

Day -3 Thesis is collated. Ensure that each copy of the thesis is in the same order. If inserting figures or tables make sure that they are inserted in the correct place according to the table of contents. Include published papers as addition evidence at the back of the thesis to the binders. The thesis must be sewn and bound with stiff covers covered with cloth. Some cover colours are not acceptable by the Librarian/University, but black, blue, maroon and green, which are the usual thesis colours are accepted by all Universities.

During binding the edges should be trimmed. On the spine of the thesis in gold lettering reading from top to bottom, the surname of the candidate, the title of the thesis (abbreviated if necessary) and the year of submission. An abbreviated title should be determined prior to lodgement of the thesis at a binder. Type out the details to be listed on the spine of thesis so there is no confusion at binding.

Books may be bound by different procedures. The most durable method is where holes are punched in the paper then pages are sewn, in the other method commonly employed, a wedge is cut on the edge of the paper, the space is sewn and glued. The latter method is somewhat inferior and may lead to a "broken spine" and subsequent dislodgement of pages. This does not occur in the first method of binding.

Most binders will take two working days to bind a thesis since they like to keep the thesis in the press overnight to ensure a satisfactory result.

If you have glued photographs smaller than A4 size onto A4 paper, the binder will introduce spacer segments in the spine so the thesis will not fan after binding.

Day -1 Thesis collected from binder. Check all copies ensuring all pages are present and bound in correct orientation. If you have not indicated which copy is produced on "acid-free paper" do so at this stage.

Day 0 Submission

Candidate: sign declaration on all copies

Supervisor/Department Head: Sign "statement by supervisor upon submission of thesis"

At Monash University the supervisor is to provide 40-50 work summary of the thesis (this appears in the graduation program). The University of Melbourne requests the graduation summary after examination of the thesis.

CHAPTER 7
THESIS SUBMISSION

7.1 Number of copies

You are requested to submit three copies of your thesis for examination if enrolled at The University of Melbourne and four copies if enrolled at Monash University. One copy remains with the University library and two copies are sent for review. After review, the first returned copy is lodged in the Department of Medicine Library, the second is forwarded to the candidate. From time to time an examiner may request to keep a copy of the thesis rather than return it. You should take this into consideration and produce more than three copies of your thesis.

Ideally you should produce five copies:

1) The University Library copy
2) A copy for examination, returned to the Department library
3) A copy for examination, returned to the candidate
4) A copy for your supervisor
5) A personal copy not submitted.
The first three copies indicate the submissions for The University of Melbourne, while the first four indicate the submission protocol for Monash University.
7.2 Supervisor's endorsement

At the time of submissions of the relevant copy numbers of the thesis, a consent form signed by the supervisor must accompany the thesis. This form certifies that the work embodied in the thesis is that of the candidate, except where otherwise acknowledged in the thesis, that the thesis is properly presented and prima facie worthy of examination. At The University of Melbourne submission, the Head of Department is also required to sign this form. At both The University of Melbourne and Monash University the candidate is also asked to sign a certificate which entails:

1. I agree/do not agree that this thesis may be made available for consultation with the University.
2. I agree/do not agree that the thesis may be made available for photocopying.
3. I note that my consent is required only to cover the three year period following approval of my thesis for the award of my degree.
Provision does exist to restrict access for longer periods if circumstances warrant such action.

CHAPTER 8
EXAMINATION

At least one month (approximately two months) prior to submission, the student and supervisor(s) should meet to discuss potential examiners and a list of examiners should be constructed. The student has the right of refusal of potential examiners. At this stage an 80 word summary of the thesis should be finalized and this, along with potential referees, are forwarded to the University for examiner selection. It is assumed that the student will not know their final examiner and that no correspondence should occur between student and members on the list of potential examiners. Monash University however, formally discloses the names of the two examiners and instructs the student not to enter into any correspondence with them.

8.1 Time spent under examination

The Office of Graduate Studies asks examiners to complete their work within 2 months, though examinations sometimes take considerable longer than this.

8.2 Recommendations of examiners

Six recommendations are available to examiners when submitting a first report on a thesis:

(a) Pass without amendment
(b) Pass subject to corrections or additions to be made to the satisfaction of the Chairperson of Examiners;
(c) Pass subject to revision of part of the thesis to the satisfaction of one or both examiners;
(d) Pass subject to clarifications in the form of written answers to questions set by the examiners, or an oral examination;
(e) Deferral of the result with permission to rewrite parts of the thesis and resubmit for a second examination;
(f) Fail with no right of resubmission.
In a re-examination, examiners are asked to record a final decision to pass or fail.
Note: Oral examinations are not held except in unusual and exceptional circumstances.

Special procedures may be adopted for oral examinations if neither examiner is able to attend. The University does allow a telephone link-up to occur (and I am aware of one such instance) whilst Monash University will appoint at least two academic members of staff to act as oral examiners. The examiner who wishes the oral to be held will supply a list of questions to be addressed to the candidate and the answer to these will be transmitted to the examiner. Under these circumstances the supervisor wil not normally be one of the academic members of staff involved in the oral examination except at the request of the examiner or examinee.

8.3 Corrections and amendments to the thesis

Theses requiring corrections must be submitted within the time specified in the letter of advice to the candidate from the Office of Graduate Studies. For a thesis requiring only minor amendments, approximately four weeks would be normally allowed. Usually, corrections and minor amendments will be incorporated into the thesis as an addenda which is inserted into the front of the thesis. Corrections and amendments to theses in the light of examiners reports are reviewed by the Chairman of Examiners.

Major amendments which are too extensive for inclusion as an addenda require revisions to be incorporated into the text.

CHAPTER 9
CONCLUSION

9.1 FINAL THOUGHTS

The writing process cannot start too early. Formulate your materials and methods sections, pencil out ideas for diagrams, make a list of abbreviations. All these "little" things will save time in the final crucial months.

Get a draft chapter to your supervisor as early as possible (that is, after you have put it through a rigorous examination) for comments. Do not hand your supervisor a complete draft of your entire thesis which you consider final - you might be in for a surprise.

Be a support network for each other. Offer to critically read someones thesis. You will benefit by identifying ways to layout a thesis (or ways not to layout) and you will polish up your punctuation and grammar skills. At the same time you will assist the person writing.

Matthew Gillespie June 1995