Your Thesis

Compiled largely from existing information by Dr Nick Hayward. See also the following websites:
University of Queensland Handbook [ Thesis Preparation];
ASMR Information [ Preparation of a PhD Thesis]

Contents: General Considerations Published Material Presentation Order and Format of Contents Final form of thesis INTRODUCTION MATERIALS AND METHODS DATA CHAPTERS FINAL DISCUSSION BIBLIOGRAPHY Text Format References Timetable for Ph.D. Submission Final Thoughts

General Considerations

A thesis should provide sufficient information to enable an examiner to determine:

1. that the investigation is deemed to make a unique contribution to knowledge in the area
2. that the investigation has been conducted with a high level of technical skill
3. that the candidate is familiar with and has employed the most suitable statistical techniques
4. that the procedures are clearly of doctoral standard
5. which work has been performed by the candidate and in which cases the results obtained by another have been analysed

It is the responsibility of the candidate to ensure that the format of the thesis complies with the directions issued by the University for the degree of Doctor of Philosophy as outlined in the University handbook. All students are therefore advised to read the conditions thoroughly.

If the thesis does not meet these requirements, the candidate may be requested to amend it, before an examination proceeds.

If there are special reasons justifying a departure from the specified format, written approval must be obtained from the head of department and the Dean of Postgraduate Students.

Consider: nothing is more frustrating to a supervisor, proof-reader, or reviewer than to find that the work lacks fundamental polish and is poorly presented.

Time initially spent on thesis layout with 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 he/she will focus on scientific relevance, logic and data, rather than spelling, grammar, punctuation and sentence construction.

The candidate should be aware of the implications of entering into a confidentiality agreement in relation to publications that might arise from the thesis. Candidates should also bear in mind that theses are lodged in the library and thus constitute archival material accessible to others. This is especially important in relation to potentially defamatory material.

A PhD thesis should be normally no longer than 100,000 words or 400 pages, including maps and diagrams, but excluding bibliography.

There should be an appropriate balance between the different parts of the thesis. In particular, the original contribution to knowledge should be clearly distinguishable from the introductory material and the survey of relevant literature.

Published Material

A thesis must have continuity in format and content.

Accordingly, relevant published material should normally be submitted as supporting papers with the thesis.

However, such materials may also be incorporated in the body of the text where they must form an integral part of the thesis.

Where published, materials are incorporated in the thesis, they must be integrated, edited and updated to eliminate repetition and inconsistency, and to ensure continuity in form and content.

Presentation

A high standard of presentation is required.

Candidates are encouraged to use a good word-processing or desktop publishing computer package combined with a high quality printer to ensure that presentation of text and any illustrative matter is both clear and attractive to the reader.

If it is necessary to include original photographs, these must be firmly bound into the thesis (if full page), or securely glued onto text pages.

As far as possible, a thesis should be free of blank pages.

International Size A4 paper should be used.

A line spacing of at least 1.5 is required.

Left and right margins should be no less than 30 mm, and top and bottom margins no less than 20 mm. (Note: to allow adequate room for binding and trimming it is recommended that the left margin should be 40mm).

Before producing final copies of a thesis for submission, the candidate should ensure that:

• all typing and other errors have been corrected
• the spelling, grammar, punctuation and choice of language are of doctoral standard
• the bibliography is complete and accurate
• references, citations and bibliography conform to the scholarly style prescribed by the Department, or as widely accepted in the discipline

Order and Format of Contents

A thesis must be preceded by a title page.

Although there is no requirement for formal approval of a thesis title, it is assumed that the title will be selected after discussion with the supervisor.

The title page of the thesis should show:

1. the title in full
2. the full name and degrees of the candidate
3. the dept in which the candidate submitted the work
4. the degree for which the thesis is submitted
5. the date of submission of the thesis

The title page should normally be followed by:

1. a signed statement of originality
2. dedications
3. quotations
4. acknowledgements
5. an abstract (ordinarily not to exceed 700 words)
6. a list of publications by the candidate on matters relevant to the thesis (may also be given as an appendix)
7. a table of contents
8. a list of all illustrations and diagrams (if illustrations and diagrams are fewer than 10 in number, this is not necessary)
9. a list of tables
10. a list of abbreviations
11. the main text
12. bibliography
13. appendices

The statement of originality signed by the candidate should declare that the work presented in the thesis is, to the best of the candidate’s knowledge and belief, original and the candidate’s own work, except as acknowledged in the text, and that the material has not been submitted, either in whole or in part, for a ***

Machine-sewn binding is preferred for temporary purposes. (Although theses bound in ring back, thermal or braced binding will be accepted, these binding methods often result in damage and pages may be lost).

A candidate may have the thesis bound at cost price by the University Printery.

Holders of an Australian Postgraduate Award or University award should refer to the Postgraduate Scholarships- General Conditions leaflet available from the Scholarships Office for information relating to the thesis allowance.

Final form of thesis

Following examination and prior to the award of the degree, a candidate must provide at least 3 permanently bound copies of the thesis to the Theses Office.

The author may request that the thesis be restricted only to staff and students of this University for up to 3 years after award of the degree.

Permanent binding consists of a full cloth stiff cover, and any additional material, such as computer disks, CDs or video-cassettes, must be included in a pocket at the back of the thesis.

The candidate’s family name and initials and a short title must be printed on the spine and front cover in gold lettering (from top to bottom).

INTRODUCTION

Prepare a general overview of the field. (This should be done as part of your 3-month HDC review).

The chief objective here is to lay the groundwork for why you will address the issues you have chosen.

If large numbers of papers have to be summarised (e.g., studies that have determined the proportion of melanomas with CDKN2A mutations) try to collate the findings into tables, rather than long lists in the text.

It is best to cite original sources, but often it is more expedient to cite a recent review(s). However, you should clearly state that it is only a review. Alternatively, do a combination of both, e.g.,

• (reviewed in Smith et al., 1999)
• (Smith et al., 1999, and references therein)
• (Jones et al., 1990; reviewed in Smith et al., 1999)

Finish this chapter with a list of hypotheses and aims.

MATERIALS AND METHODS

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

Consider: your thesis may often form a lab. manual from which others may attempt to repeat your methods - therefore make them detailed and comprehensive.

It is often useful to have a general Materials and Methods chapter (Chapter 2) and to also include additional chapter-specific Methods as subsections of each chapter

When first mentioning a chemical you should provide the supplier’s name and place of origin in full, e.g.,

sodium chloride (Sigma Chemical Co. Ltd, St Louis, MO, USA).

Any references to Sigma thereafter should be:

(Sigma Chemical Co. Ltd).

Remember to refer to the site of the company’s head-office rather than the local distributor, e.g.,

Amersham International, Buckinghamshire, UK

not,

Amersham International, Sydney.

If you use samples from patients they should be de-identified and numbered in such a way that they can be tracked throughout the thesis. Be consistent with their numbering.

DATA CHAPTERS

Should have their own introductions that pertain specifically to the work carried out in each chapter, however, attempt to link them to previous chapters to show a continuous theme.

It may be useful to restate the original aim that the work in the chapter addresses.

Have discussion and conclusions specific to that chapter, and try to link outcomes to those of preceding chapters (once again maintaining a common thread).

In terms of experimental work be clear of what is a suitable end-point for the chapter, i.e., have you succeeded in your aim(s)?

Make sure you are thinking about final thesis figures/tables all the time, e.g.,

• remember to have a negative if you think you’ll need to print a particular gel photo
• check you have data/photos of all relevant samples
• make sure you have completed all of the requisite controls
• statistically analyse your data to see whether they are significant – you may need to analyse more *** r to all parts of the figure (i.e., each lane, or each sub-component) and state units/scale if relevant

Remember to label the figures comprehensively.

Figure pages should also be numbered.

FINAL DISCUSSION

This is a very important part of the thesis since it gives you the opportunity to summarise all of the work you have done and to put it into context with the rest of the literature.

You should coalesce and condense your thoughts so that you are able to make clear and concise statements about the results you have obtained, what their implications are, and how they might impact on the rest of the field.

Revisit your aims and hypotheses, and demonstrate how your investigations have addressed them. If you feel your findings have proven a particular hypothesis then state his clearly.

An important part of this chapter is to detail any (and all) shortcomings of your project. Rarely does a candidate achieve everything they set out to achieve – discuss why you fell short of the mark in specific areas and what approaches you would take to overcome them if you were to redo the work.

If new technologies have become available since you started your PhD then discuss them and outline how they might be used to address the problems you have tackled.

Finally, suggest other work that could be undertaken to further enhance your field of interest – in particular, work that obviously follows on from your findings.

BIBLIOGRAPHY

Style

Any source from which information is derived, must be clearly, concisely and accurately cited.

There are no University rules for the citation of references, although some departments and some professions prescribe a style appropriate to that discipline.

Where a department has not prescribed a style, advice should be taken from the supervisor.

Bibliographic style should be established early in the preparation of a thesis to avoid time-consuming work at final manuscript stage.

It is essential that the style adopted be followed consistently.

Tip: use PubMed style but remember to:

1. delete irrelevant information (e.g., month, part number)
2. include full stops at the end of the citation
3. add missing authors’ names if the list ends in "et al."

Optional: change fonts of journal names (italic) and volumes (bold).

A list of style manuals is given below:

The Chicago Manual of Style: The Essential Guide for Writers, Editors, and Publishers. (14th ed.) Chicago: University of Chicago Press (1993).

Gibaldi, J. & Franklin, P. (1995). MLA Handbook for Writers of Research Papers (4th ed.) New York: Modern Language Association of America.

Gibaldi, J. & Lindenberger, H. (1998). MLA Style Manual and Guide to Scholarly Publishing (2nd ed). New York: Modern Language Association of America.

Trimmer, J. (1998). The Essentials of MLA Style: A Guide to Documentation for Writers of Research Papers. New York: Modern Language Association of America.

Trimmer, J. (1993). Guide to MLA Documentation With an Appendix on Apa Style: With an Appendix on Apa Style (English Essentials) (3rd ed.). New York: Modern Language Association of America.

Turabian, K.L., Grossman, J. & Bennett. (1996). A Manual for Writers of Term Papers, Theses, and Dissertations (Chicago Guides to Writing, Editing, and Publishing) (6th Rev edition), Chicago: University of Chicago Press.

List authors alphabetically, then chronology.

Ensure that all references cited in the text are included in the bibliography, and that the names and dates of the citations are consistent.

Content of citation

The minimum citation for books must include author(s), title, edition (if other than first), place of publication, publisher, date of publication and relevant pages.

The citation for periodical articles must provide at least author(s), title of article, name of periodical, volume number, part number (if volume is not paginated continuously), date of publication and relevant pages.

Journal Abbreviations

If the full titles of periodicals and other serials are not used, abbreviations should be those used in the World List of Scientific Periodicals published in the years 1900-1960 (4th ed. Michigan: Arbor, 1997), the Bibliographic Guide for Editors and Authors (Washington: American Chemical Society, 1974) or the International List of Periodical Title Word Abbreviations (New York: Standards Committee 239 American National Standards Institute, 1970).

Text Format

Spelling

Use English not American spelling, e.g.,

Use a spell-checker, or better still, use WORD 6.0 as it shows you on-screen what words are incorrect or not part of its vocabulary (note: add words to the dictionary once you are certain they are correct)

Use a proof-reader who is good at spelling and grammar.

Hyphenation

A hyphen should be used in adjectival descriptions,

e.g., well planned or, well-planned
ill disguised or, ill-disguised
UV treated or, UV-treated
cyclin dependent or, cyclin-dependent

Note: usage depends on context, i.e., whether or not the compounds come before or after the subject/object.

Hyphens are often used to tie two or more words together,

e.g., up-to-date, out-of-sorts.

Hyphens are required in number compounds,

e.g., twenty-four, 80-fold, four-fifths, thirty-something, pre- 1770, ten-year-old.

Hyphens are required to differentiate meanings,

e.g., re-form versus reform
re-lay versus relay

Be wary of hyphens at the end of lines,

e.g., do not separate – 70oC

(Note: use the "widow/orphan" function of word-processing packages).

Latin

Use italic.

Abbreviations

General rules:

• Place full-stops at the point of truncation of the word.
• Examples: e.g., i.e., et al., etc., Prof.,

Note: if an abbreviation is created by deleting the middle letters of a word, do not include a full-stop.

Examples: Dr, Mr, St, Rd,

Do not use apostrophes in plurals.

Too frequently are abbreviations altered between chapters due solely to the time difference in writing.

Tip: when writing have a separate sheet of paper on which you can add the abbreviations that you are using in the thesis and refer back to this list to adhere to them so you are consistent throughout the text.

(This will provide the basis for your alphabetical listing of abbreviations in the thesis).

Generally, once you have used an abbreviation do not go back to writing the word(s) in full, unless it is for dramatic effect, e.g., in your conclusions, or to stress a point.

Remember when you first use an abbreviation of a chemical you should supply the name in full, followed by the abbreviation in parenthesis,

e.g., sodium dodecyl sulphate (SDS)

As a general rule in an acronym each letter is capitalised.

e.g., SDS, CDK, UVR.

There are exceptions when an acronym has become a word in its own right,

e.g., radar, laser, scuba.

Species names

Escherichia coli should be abbreviated to E. coli not E. coli or E. Coli.

Restriction enzyme names are derived from micro-organisms and should therefore be in italic.

Enzyme numbers are in Roman numerals not Arabic.

Note spacing.

e.g., EcoR I not EcoRI or EcoR1 or EcoRI
Xho II not XhoII or Xho 2 or Xho II

Note: there are some tricky ones, e.g., DIR>

(i.e., things to be introduced)

a semicolon denotes a longer pause than a comma (modern usage has all but replaced this with a dash).

Learn the appropriate uses of commas.

Apart from creating pauses they can also change the meaning of a sentence.

Never put them before parentheses.

Grammar

Use WORD 6.0 as it shows you on-screen what phrases are incorrect.

The thesis is to be written in the "past tense".

Avoid statements to yourself,

e.g., "I undertook an analysis of……….."

Also avoid the use of "we".

e.g., "We undertook an analysis of……….."

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".

Learn the appropriate uses of "which" and "that".

"That" is used in a defining clause (i.e., adds essential information), whereas "which" is appropriate for a non-defining clause (i.e., simply provides additional non-essential information), e.g., compare:

Let’s buy the kind of cheese that she likes best.
Let’s buy brie, which she likes the best.

Note: the meaning of a sentence can be drastically altered by differential usage of "that" and "which", e.g., compare:

Rice that is grown in Australia is the staple diet of Asia.
Rice, which is grown in Australia, is the staple diet of Asia.

Remember when to use "were" and "was".

"Were" denotes a plural, the most common mistake is to use "was" after units of measurement,

e.g., 5 ml was added 5 ml were added

(Tip: say the abbreviated units aloud in full).

Avoid inappropriate capitalisation.

In general, avoid splitting infinitives.

An infinitive is the basic form of a verb, usually preceded by "to", e.g., to walk, to eat, to do.

When an infinitive is broken by an adverb or phrase immediately following the "to", it is said to be "split".

e.g., to walk slowly
to slowly walk

Nomenclature

Genes versus proteins

A gene name/symbol should be in italic, while the protein product is not, e.g.,

CDKN2A p16
TP53 p53

Note: there are often subtle differences between gene and protein symbols, e.g.,

VEGFR1 VEGFR-1
VEGFB VEGF-B

Remember human and murine symbols are different, i.e., for humans use block capitals and for mice a capital for only the first letter, e.g.,

SOD2
Sod2

Remember what type of molecule you are discussing (DNA, RNA, protein) and be accurate with your meaning. A common error is to give a trait of one type to another,

e.g., "actin primers were used to amplify…."

Actin is a protein, therefore you can’t make primers to it. (Correct wording: actin cDNA primers……., or primers to the actin gene…….).

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.

References

In the 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.

Use Reference Manager (or equivalent) as this program will greatly reduce collating time.

Recommendations:

Blah, blah, blah, ................ as previously reported (Smith and Jones, 1970; Smith et al., 1972).

Notes:

• following the authors’ names a comma should appear, then the year of publication
• a semicolon should be used between references
• for more than two authors use the abbreviation et al. (a full stop should follow "al." since this is an abbreviation)
• when quoting more than one reference, references should be ordered chronologically then alphabetically
• if one author has more than one publication in a given year use letters as suffixes,

e.g., "Smith et al., 1981a, b, c".

(Smith et al., 1981a denotes the first cited reference of this series by the author)

The study by Smith and Jones (1970)……
The study by Smith et al. (1972)……..

(Note: when using "et al." in the text do not include commas immediately before parentheses).

Timetable for Ph.D. Submission

-4 to -3 years:

• Enrolment and commencement of candidature.
• Begin literature review, materials and methods and bibliography.

-3.75 to –2.75 years:

• Three-month review: submit a literature review and orally present your research outline (see HDC requirements).

-3 to - 2 years:

• One-year review: orally present your work to date and indicate what problems you have encountered (if any). Outline the work you have remaining.
• Confirmation of candidature. (see HDC requirements)

-1 year:

• Final plan of thesis chapters to be completed.
• Final phase of experimental work to commence.
• Potential extensions of candidature and scholarships may be considered - consult with your supervisor.
• Start thinking about post-doctoral positions.

-6 to -4 months:

• Final review: this is primarily to determine that you have completed sufficient work (and of appropriate quality) for a PhD.
• Commence writing in earnest.
• Finalise all figures.
• Apply for post-doctoral fellowships.
• Public presentation of research findings by seminar.

-4 to -1 month:

• Writing and re-writing work corrected by your supervisor and colleagues.

-1 month:

• Notify Head of Department of your intention to submit.
• Give "finished" chapters to a proof-reader.

Day -14 to –7:

• Final corrections to be completed.
• Check that printers are working and binders will be open over the next 1-2 weeks.

Day –6:

• Make final amendments.
• Adjust pagination.
• Formulate table of contents.

Day –5:

• Final print-off of thesis.
• Print off top copy and check the entire thesis paying particular attention to pagination.
• Make sure that the table of contents is correct with respect to the final page numbers.

Day –4:

• Collate all pages to be taken to the printer.
• Ensure your copies will be printed on acid-free paper.
• Print the desired number of copies.

Day –3:

• Collate all copies of the thesis.
• If inserting figures or tables make sure that they are inserted in the correct place.
• Take copies to the binder for temporary 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 may introduce spacer segments in the spine so the thesis will not fan after binding.

Day –1:

• Collect thesis from binder.
• Check all copies ensuring all pages are present and bound in correct orientation.

Day 0:

• Sign declaration on all copies.
• Get supervisor/Department Head to sign "statement by supervisor upon submission of thesis" form.
• Submit thesis.

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.

These things will save time in the final crucial months.

Get draft chapters to your supervisor as early as possible (after you have put them through rigorous examination) for comments.

Do not hand your supervisor a complete draft of your thesis that you consider final - you might be in for a surprise!

Be a support network for each other.

Offer to critically read someone’s thesis. You will benefit by identifying ways to layout a thesis (or ways not to!) and you will polish up your punctuation and grammar skills. At the same time you will assist the person writing.

Guides to thesis writing:

Anderson, J. & Poole, M. (1998). Assignment and thesis writing. (3rd ed.) Brisbane: John Wiley & Sons.

Mauch, J.E. & Birch, J.W. (1998). Guide to successful thesis and dissertation: a handbook for students and faculty. (4th ed., rev.) New York: M.Dekker.

Locke, L.F., Spirduso, W.W. & Silverman, S.J. (1993) Proposals that work: a guide for planning dissertations and grant proposals. (3rd ed.) California: Sage Publications.

Rountree, K. & Laing, T. (1996). Writing by degrees: a practical guide to writing theses and research papers. Auckland: Longman.

Glatthorn, A.A. (1998). Writing the winning dissertation: a step-by-step guide. California: Corwin Press.

Evans, D.G. (1995). How to write a better thesis or report. Victoria: Melbourne University Press.