Thesis & Report Guide

Bob Smoot
Smoot College
University of Oxford

Supervised by
Professor What Whoever
Submitted: Crinklemas Term,
May 31, 2012

This thesis is submitted to the Department of Engineering Science,

University of Oxford, in partial fullment of the requirements for the
degree of Doctor of Philosophy
 Declaration
I declare that this thesis is entirely my own work, and except where

otherwise stated, describes my own research.

B. S. Smoot,

Smoot College
 Dedication
This thesis is dedicated to ...

This is optional and should only be included in a DPhil. Do not include

this section for PRS, MSc, MEng, Summer Reports etc.

 Abstract

Insert a one page abstract of the work here ...

This should be just a couple of paragraphs to set the scene and provide the

(clinical) motivation, then describe your key contributions to scientic knowl-

edge and key results.

Writing an ecient abstract is dicult but is worth it because it increases the

impact of your work by enticing people to read your publications and allows

automated search engines (which sometime use only the title and abstract)

to index your work for accurate discovery (and hence citation). The following

advice (borrowed partially from Philip Koopman's 1997 website at Carnegie

Mellon University, also applies to any scientic article.

First, you need to lay it out in a logical order, like your thesis - intro/motivation,

methods, results, conclusion. Some journals (particularly medical journals)

require specic titles in the abstract, although most engineering journals do

not. The following key elements should be in your abstract:

ˆ Motivation: Why do we care about the problem and the results? If the

problem isn't obviously interesting it might be better to put motivation

rst; but if your work is incremental progress on a problem that is widely

recognized as important, then it is probably better to put the problem

statement rst to indicate which piece of the larger problem you are

breaking o to work on. This section should include the importance of

your work, the diculty of the area, and the impact it might have if

successful.

ˆ Problem statement: What problem are you trying to solve? What is

the scope of your work (a generalized approach, or for a specic situa-

tion)? Be careful not to use too much jargon. In some cases it is appro-

priate to put the problem statement before the motivation, but usually

this only works if most readers already understand why the problem is

important.
 ˆ Approach: How did you go about solving or making progress on the

problem? Did you use simulation, analytic models, prototype construc-

tion, or analysis of eld data for an actual product? What was the extent

of your work (did you look at one application program or a hundred pro-

grams in twenty dierent programming languages)? What important

variables did you control, ignore, or measure?

ˆ Results: What's the answer? Specically, most good engineering papers

conclude that something is so many percent more accurate, sensitive,

specic, faster, or otherwise better than something else. Put the result

there, in numbers. Avoid vague, hand-waving results such as very,

small, or signicant. The latter word, signicant is reserved for

statistical analysis only. If you do use `signicant, quote the p-value and

the test (as well as the data on which the test was performed). Compare

your results (numerically) to the best or benchmarks in the eld. If you

must be vague, you are only given license to do so when you can talk

about orders-of-magnitude improvement. There is a tension here in that

you should not provide numbers that can be easily misinterpreted, but

on the other hand you don't have room for all the caveats.

ˆ Conclusions: What are the implications of your answer? Is it going

to change the world (unlikely), be a signicant win, be a nice hack

(i.e. shortcut that saves time, money, eort), or simply serve as a road

sign indicating that this path is a waste of time. (All such results are

useful.) Are your results general, potentially generalizable, or specic

to a particular case? Do not over-state your case. Don't claim success

outside of the domain of your experiments.

Note that an abstract must be a fully self-contained description of the work

(thesis, paper, report). It can't assume (or attempt to provoke) the reader

into ipping through looking for an explanation of what is meant by some

vague statement. It must make sense all by itself. Some points to consider

include:

ˆ Meet the word count. If your abstract runs too long, either it will be

rejected or someone will take a chainsaw to it to get it down to size.

Your purposes will be better served by doing the dicult task of cutting

yourself, rather than leaving it to someone else who might be more in-

terested in meeting size restrictions than in representing your eorts in

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 the best possible manner. An abstract word limit of 150 to 200 words is

common.

ˆ Include scientic limitations of study. Any major restrictions or limi-

tations on the results should be stated, if only by using weasel-words

such as might, could, may, and seem.

ˆ Abbreviations. You do not need to dene common abbreviations for a

given journal. Generally check with the journal. In your thesis you must.

Do not dene abbreviations in a title, only in the text, the rst time it

is used. If you only use it once, there's no need for an abbreviation.

Remember that the abstract is self contained, so any abbreviations will

have to be redened in the main text of the thesis or article.

ˆ Include key words and phrases. Think of a half-dozen search phrases

and keywords that people looking for your work might use. Be sure that

those exact phrases appear in your abstract, so that they will turn up

at the top of a search result listing. Try not to use colloquialisms, or

over-use buzz-words or your article will sound like you are trying to be

fashionable, rather than accurate.

ˆ Consider the context and readership. Usually the context of an article is

set by the publication in which it appears (for example, IEEE Computer

magazine's articles are generally about computer technology). But, if

your paper appears in a somewhat non-traditional venue, be sure to

include in the problem statement the domain or topic area to which it

is really applicable.

ˆ Keywords. Some publications request keywords. These have two pur-

poses. They are used to facilitate keyword index searches, which are

greatly reduced in importance now that on-line abstract text searching

is commonly used. However, they are also used to assign papers to review

committees or editors, which can be extremely important to your fate.

So make sure that the keywords you pick make assigning your paper to a

review category obvious (for example, if there is a list of conference top-

ics, use your chosen topic area as one of the keyword tuples). You may

also be required to enter numerical codes (such as in the Physics and

Astronomy Classication Scheme (PACS) system),indicating the areas

which are associated with your research

So in conclusion, your abstract should be much shorter than this abstract

appears to be (because it's not an abstract). For an example of a good

6
abstract, see below for an article I published in the Journal of Biomedical

Informatics. Note that it was for a semi-clinical journal, so the complex

techniques are brushed over because the medical doctors reviewing this would

not be that interested in the specic techniques in the abstract. You cannot

do this for a technical journal - you will have to name the types of algorithms

you used, like `four-layer perceptron with a sigmoid activation function'. Note

also that ECG is not dened, because it is so widely understood in clinical

informatics to mean `Electrocardiogram'.

Reducing false alarm rates for critical arrhythmias using the arterial
blood pressure waveform.

Over the past two decades, high false alarm (FA) rates have remained an

important yet unresolved concern in the Intensive Care Unit (ICU). High FA

rates lead to desensitization of the attending sta to such warnings, with

associated slowing in response times and detrimental decreases in the quality

of care for the patient. False arrhythmia alarms are commonly due to single

channel ECG artifacts and low voltage signals, and therefore it is likely that

the FA rates may be reduced if information from other independent signals is

used to form a more robust hypothesis of the alarm's etiology.

A large multi-parameter ICU database (PhysioNet's MIMIC II database) was

used to investigate the frequency of ve categories of false critical (red or

life-threatening) ECG arrhythmia alarms produced by a commercial ICU

monitoring system, namely: asystole, extreme bradycardia, extreme tachy-

cardia, ventricular tachycardia and ventricular brillation/tachycardia. Non-

critical (yellow) arrhythmia alarms were not considered in this study. Mul-

tiple expert reviews of 5386 critical ECG arrhythmia alarms from a total of

447 adult patient records in the MIMIC II database were made using the

associated 41,301 h of simultaneous ECG and arterial blood pressure (ABP)

waveforms. An algorithm to suppress false critical ECG arrhythmia alarms

using morphological and timing information derived from the ABP signal was

then tested.

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An average of 42.7% of the critical ECG arrhythmia alarms were found to be

false, with each of the ve alarm categories having FA rates between 23.1%

and 90.7%. The FA suppression algorithm was able to suppress 59.7% of

the false alarms, with FA reduction rates as high as 93.5% for asystole and

81.0% for extreme bradycardia. FA reduction rates were lowest for extreme

tachycardia (63.7%) and ventricular-related alarms (58.2% for ventricular b-

rillation/tachycardia and 33.0% for ventricular tachycardia). True alarm (TA)

reduction rates were all 0%, except for ventricular tachycardia alarms (9.4%).

The FA suppression algorithm reduced the incidence of false critical ECG ar-

rhythmia alarms from 42.7% to 17.2%, where simultaneous ECG and ABP

data were available. The present algorithm demonstrated the potential of

data fusion to reduce false ECG arrhythmia alarms in a clinical setting, but

the non-zero TA reduction rate for ventricular tachycardia indicates the need

for further renement of the suppression strategy. To avoid suppressing any

true alarms, the algorithm could be implemented for all alarms except ventric-

ular tachycardia. Under these conditions the FA rate would be reduced from

42.7% to 22.7%. This implementation of the algorithm should be considered

for prospective clinical evaluation. The public availability of a real-world ICU

database of multi-parameter physiologic waveforms, together with their asso-

ciated annotated alarms is a new and valuable research resource for algorithm

developers.

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 Acknowledgements

Write something along the lines of:

This thesis would not be possible without ...

Include funding agencies, and any scholarships you won, people who helped

you (your supervisor for instance, but also colleagues).

This is not an Oscar ceremony, don't go on at length.

Contents
1 Introduction 1
1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1.2 What should be in Chapter 1? . . . . . . . . . . . . . . . . . . . . . . . . 1

1.3 AT X?
Typesetting: Word or L . . . . . . . . . . . . . . . . . . . . . . . . 2
E
1.3.1 AT X . . . . . . . . . . . . . . . . . . . . . . . . .
Reasons to use L 3
E
1.3.2 What about comments and track changes? . . . . . . . . . . . . . 3

1.4 AT Xsoftware
Installing the L . . . . . . . . . . . . . . . . . . . . . . . . . 4
E
1.4.1 Editor choice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

1.4.2 What about spell-check? . . . . . . . . . . . . . . . . . . . . . . . 4

1.4.3 Versioning, back-ups and roll-backs . . . . . . . . . . . . . . . . . 4

1.5 Lab diary: paper, emails or Google docs? . . . . . . . . . . . . . . . . . . 5

1.6 Sensitive data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

1.7 This template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

1.8 Format and length of document . . . . . . . . . . . . . . . . . . . . . . . 8

1.8.1 CDT Summer Report . . . . . . . . . . . . . . . . . . . . . . . . . 8

1.8.2 4YP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

1.8.3 M.Sc. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

1.8.4 PRS Transfer report . . . . . . . . . . . . . . . . . . . . . . . . . 11

1.8.5 D.Phil. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

2 Previous Work in the Field 15

2.1 Content of chapter 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

2.2 Chapter layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

2.3 Internal (cross) referencing: the label command . . . . . . . . . . . . . 15

2.3.1 Equations, tables and gures . . . . . . . . . . . . . . . . . . . . . 16

2.3.2 Indexing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

2.4 External referencing and bibliography . . . . . . . . . . . . . . . . . . . . 16

2.4.1 Automated reference search and generation: Jabref . . . . . . . . 17

2.5 Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

i
 2.5.1 Labels, Legends, Units and Captions . . . . . . . . . . . . . . . . 18

2.5.2 Figure format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

2.5.3 Combining gures . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

2.5.4 Common gure mistakes . . . . . . . . . . . . . . . . . . . . . . . 19

2.6 Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

2.7 Equations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

2.7.1 In-line equations . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

2.7.2 Numbered equations . . . . . . . . . . . . . . . . . . . . . . . . . 23

2.7.3 Equation arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

2.8 Footnotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

2.9 Appendices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

2.10 Abbreviations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

2.11 Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

2.12 Symbol list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

3 Data Used in Thesis and Preprocessing 27

3.1 Plagiarism and collusion . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

3.2 Authorship . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

3.3 Acknowledgments and funding bodies . . . . . . . . . . . . . . . . . . . . 29

3.4 References, citations and `personal communications' . . . . . . . . . . . . 30

3.5 IRB/Ethics approval . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

3.6 Double publishing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

3.7 Copyright . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

3.8 Conicts of interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

3.9 Patents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

3.10 Source code and open source . . . . . . . . . . . . . . . . . . . . . . . . . 34

3.11 Presentations, conferences and other `publications' . . . . . . . . . . . . . 35

3.12 Sharing results before publication . . . . . . . . . . . . . . . . . . . . . . 35

3.13 Disclaimer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

4 Clever things I did to the data part 1 37

5 Clever things I did to the data part 2 38

6 Clever things I did to the data part 3 39

7 Conclusions and future work 40

A Timeline for completion 41

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B List of publications and presentations 43

C Abbreviations and glossary of terms 45

C.1 Abbreviations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

C.2 Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

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List of Figures
1.1 AT X. Taken
Graph to show relative estimated time wasted using Word or L E
from:

http://www.pinteric.com/miktex.html . . . . . . . . . . . . . . . . . 2

2.1 Combining several plots into one . . . . . . . . . . . . . . . . . . . . . . 20

iv
List of Tables
2.1 Variable Boundaries for physiological parameters used in this study. . . . 22

v
Chapter 1
Introduction
1.1 Introduction
The point of this `thesis' is to provide some guidance on how to lay out and typeset your

thesis. It also provides some tips on the general process, but is not a guide to the rules

and regulations governing your research, or how you should organize yourself.

Disclaimer: First you should remember this document (and template) is only a guide,

not a dictator. Parts may not suit you, be relevant to you or may be out of date. Details

will vary based on your report type, supervisor and sub-department. Always check the

details with your department before blindly following this guide. I take no responsibility

for any use of the information provided here. it was approximately correct when I wrote

it, but things change and I don't have the time to constantly update this. If you nd an

error, do email me, and I'll add it to my long ToDo list.

1.2 What should be in Chapter 1?

For biomedical engineering thesis is is normal to begin Chapter 1 by providing the clinical

background and motivation for the problem plus a review of existing approaches to solve

the problem you are introducing. Make sure to dene the problem. The chapter often

1
Figure 1.1: A
Graph to show relative estimated time wasted using Word or L TEX. Taken from:

http: // www. pinteric. com/ miktex. html

ends with a description of the contents of the rest of the thesis, explaining the 'story' you

are going to tell.

1.3 Typesetting: Word or LATEX?

Well I'll be clear. If you use some wysiwyg (what you see is what you get) type-setting

AT Xby at least
tool (like Word or Open Oce), I predict you will wish you had used L E

the end of your second year, if not before. Why? See gure 1.1.

Word is a practical tool for writing short and simple documents but becomes too

complex or even unusable when using a wysiwyg system. Granted, there's a small eort

required up-front to learn the typesetting commands, but hopefully I've included an

example of one of everything that you will need in this document.

2
 The only time a wysiwyg type-setting tool is practically useful is for working with

people who are going to contribute signicantly to your paper and you are not using

mathematics or many images. Some clinical journals may even require you to use Word.

AT X.
However, in general, most journals accept (and like) L E

1.3.1 Reasons to use LATEX

OK - so here are a few specic reasons ... there are many more, but you'll need to

AT Xrst.
understand some more about L E

1. Powerful and simple bibliography tools - combined with Jabref (see section 2.4.1)

you may never have to write out a reference ever again.

2. Portability and re-usability. My latex from 1989 still works. Converting wysiwyg

documents from 2 years ago is problematic. In fact, when I swap from my laptop

to desktop, (both running XP, although one virtualized) the small changes in Oce

versions mean my document formatting changes each time. You will reuse parts of

your thesis as you move from the CDT Summer Report to the PRS transfer report

to the main D.Phil. thesis. Each time you will likely reuse parts of your thesis.

AT X.
Placing parts of your thesis into a journal template is far easier in L E

3. Unmatched professional consistent typesetting.

4. Quality of images. You are forced to make your images and text separate. This

leads to far superior images that are not altered in quality by the wysiwyg system.

5. Vastly superior exibility when dealing with images, tables etc.

6. Easy to comment out sections and restore later, and add notes to self.

1.3.2 What about comments and track changes?

Yes - track changes are useful, so use it with Word or Google Docs, etc., when required,

but only you are the maintainer of your thesis. No-one but you should be editing your

3
thesis, so there's no need for it. Use a source code control system (like subversion) for

your thesis, and you will never lose a le or comment again.

However, you may want to add comments (and your supervisor or helpful post-doc

may be encouraged to do so) by using the custom commenting commands in the main

template. These are \todo{} (TODO: red) and \comment{} (green), Anything placed in
the curly braces of these commands will be colour coded accordingly. They are then easy

to nd later and help your supervisor know what are you comments and questions.

Anyway, Acrobat Reader (version 10 and above) allows you to add comments directly

to the PDF, so there's really little excuse to use track changes now.

1.4 Installing the LATEXsoftware

http://www.latex-project.org/Latex-Project.org. Operating system-specic instal-

lations can be found here: http://www.latex-project.org/ftp.html. An example

distribution that has proved successful is MikTex: http://miktex.org/.

1.4.1 Editor choice

AT Xdistributions include a text editor, (including MikTex), but you may want
Many L E

to consider a more powerful editor like Emacs: http://www.gnu.org/software/emacs/.

As with code editors, you may nd that syntax highlighters are useful.

1.4.2 What about spell-check?

This is important - but almost any editor has one. A classic tool is iSpell:
http://www.ssc.wisc.edu/~dvanness/ispell.htm. This works well with Emacs.

1.4.3 Versioning, back-ups and roll-backs

Make an o-site backup of your code, thesis, annotations, lab notes etc. and make a note

in your calendar to do this daily (or at the least, weekly). (Assume your hard disk will

4
crash and you lose your USB back-up one week before your report is due.) Do not back

up data that can be regenerated - it become unmanageable and it wastes disk space. Just

back-up the scripts to generate the derived data.

If you do not have access to a source code control system, then I suggest you use

something like dropbox.com - this is an excellent way to make incremental back-ups of

your les and roll-back to earlier versions. You can also share the directory with your

supervisor/collaborators.

If you are wondering what exact changes took place to a chapter or piece of source

code, try using kdiff (http://kdiff3.sourceforge.net/).

kdiff is an excellent tool for comparing two versions of the same code to see what

has actually changed. This is particularly good for tracking incremental versions, and

merging versions that you made on dierent computers. (You can just drag and drop the

changes from one doc to the other.)

1.5 Lab diary: paper, emails or Google docs?

For physical experimental work you may nd it is better to keep lab notes in paper form.

A lab book should be dated and initialed each day (in case there is a dispute about

when an idea was rst conceived). Some funding agencies require your lab diaries to be

co-signed each day too!

For computational-based research, a better option can be a digital lab book. Google
docs make an excellent backed-up progress report with automatic time stamping and

authorship. They are great for collaboration and tracking changes. (You can even embed

AT Xequations in the document.)

L E

Email is another way to back up such information, but is not good for versioning,

roll-backs, versioning and collaboration.

Whichever method you choose to track your progress, and organize your daily thoughts,

you should make sure that you get in the habit of doing this. Consult your supervisors

5
though - they may not be happy with the above suggestions, particularly if you may be

dealing with intellectual property or sensitive data.

Note that you should not use these methods to record sensitive informa-

tion. See section 1.6.

1.6 Sensitive data

Sensitive data, such as that restricted by a non-disclosure agreement or identiable patient

data (e.g. data containing names, dates, retina images, ngerprints, full face photos, etc.)

should not be emailed, backed up on public servers, or copied to non-secure/unencrypted

hard drives or portable media. This includes your laptop or desktop computer. You

should encrypt a partition of your hard drive and make sure the data are copied only to

this partition. Above all, check with your supervisor regarding the policy on where data

should be stored. Some data should not be taken out of the location from where it was

recorded.

1.7 This template

This template is based upon a combination of templates sent to me by various students

and post-docs, things I found on the Internet, and my own experience and papers/thesis.

I credit no-one, including myself, as I consider it 'anonymous creative-commons'. As

far as I know, there is no standard Oxford thesis template or guidelines on how to lay

out these documents. So I've done what all students do, and taken an aggregate of the

most recent accepted theses and added my own thoughts. Feel free to tweak, but make

sure you check this in the same manner to ensure you don't stray too far (0.1 standard

deviations?) from the accepted 'norm'.

This template is intended to be a general all-purpose report framework, covering

4th year projects (4YPs), CDT Summer Reports, Probationary Research Status (PRS)

6
 1 2
Transfer Reports , M.Sc., M.Phil., and D.Phil . This means you will need to comment

out certain sections that do not relate to your report type. The in-line comments in the

AT Xle will explain if you need the relevant section or not.

master L E

The template is divided into several les you will need to edit:

ˆ template_surname_report_type.tex - This is the main le (which you compile)

and will automatically include all the other les. You do not need to edit this unless

you want to. When you compile this template, you will generate a PDF document

called the same thing as the main template le. I.e. -

template_surname_report_type.pdf. Make sure you rename this main template

to something name- and report- specic (e.g. Einstein_MSc.tex) so that when

you send the PDF to your supervisor, it is self-explanatory.

ˆ declaration.tex - A declaration that this is all your own work, except where

indicated.

ˆ dedication.tex - Self-explanatory.

ˆ abstract.tex - The summary of what you did, plus key achievements.

ˆ acknowledgments.tex - A list of all those that helped you.

ˆ chapterN.tex - The main chapters of the thesis (where N= 1, 2, ..., 6 or more).

ˆ conclusions.tex - Self-explanatory.

ˆ gant.tex - A Gant chart showing the major tasks and when you will do each one

up to the end of the thesis.

ˆ publist.tex - A list of your publications as a result of the thesis.

ˆ glossary.tex - A list of abbreviations and denitions.

1 At the end of your rst year of your D.Phil. you are required to present a report describing
your rst year of research, and a proposal for the next 2+ years to complete the D.Phil.
2 Ph.D.

7
 ˆ refs.bib - The master le containing all the publications you want to cite.

1.8 Format and length of document

Note that these are subject to change, but the guidelines were probably correct as of June

2010. Check with your department to make sure - don't take this document as the nal

word.

To change this template from its current single spaced version, to the 11pt Arial text

required for some reports change the `documentclass' declaration in the main TeX le to

read:

\documentclass[bibliography=totoc,11pt,a4paper,english,oneside]{scrbook}
\renewcommand{\rmdefault}{phv} % arial fonts
\renewcommand{\sfdefault}{phv}
\linespread{2} % for double spacing

1.8.1 CDT Summer Report

AT Xtemplate.
You must use the standard IEEE Transactions on Biomedical Engineering L E

The report must be between 8 and 12 pages long (including abstract, all appendices, etc.).

Do not attempt to change the font size/type or margins, or you will be ask to rectify the

issue, adhere to the page limit and resubmit.

Do follow the standard style instructions, and pay particular attention to placing the

correct information in the right sections. Results should not appear in the methods, and

methods should not appear in the introduction or the results sections. It seems obvious,

but I see it all the time. The layout is the standard scientic form:

ˆ Abstract: See the abstract description at the start of this report

ˆ Introduction: Set out what the motivation for the study is, and briey what you

did (at a high level).

8
 ˆ Background: Detail what others have done before as a benchmark.

ˆ Methods: Describe your scientic methods in a logical manner. Do not list a

chronology of your thoughts and every detail that didn't work. Step back and

think how you can present the work in the most coherent and succinct manner. Do

not give away any results here.

ˆ Results: List your results in the same order as your methods, with corresponding

sections. There must be a methods section for every result section. Do not analyse

or interpret them at this stage. Do make sure you describe the results in enough

detail, and make sure everything is dened.

ˆ Discussion: Now you can interpret the results and discuss them in the context of the

background work. Compare your results to those of the rest of the eld and explain

why they are better or worse, and whether the results are directly comparable. Also

list the limitations of your study and what the next logical steps are.

ˆ Conclusions: Sum up the study and results, and its relevance importance.

ˆ Acknowledgments: Include the exact acknowledgments as described. Include all

funding bodies and any contributors not listed as an author.

1.8.2 4YP
These are expected to be 50 pages, (including all appendices, frontmatter etc.), although

they can be shorter. Content over quantity. In March 2011, these were the instructions

mailed out (which may have changed of course):

Printing: The deadline for submitting a report to the Engineering Science Print

Room (Thom Building room 1.03) for printing by the Department is Friday of week 2 of

Trinity Term. You can submit your report for printing in the form of a WORD, pdf or

postscript le (e-mail to printroom@eng.ox.ac.uk, or call by the print room in person).

9
 You are allowed a maximum of 10 pages of colour printing per copy of your report.

(For joint reports each student contributing to the report is entitled to 10 pages of colour

within each copy of that report.) If you have more you are liable to be charged at a rate

of 25p per page. Even a single coloured line on a graph will be counted as a colour page!

It is not permissible to use spare funds from your project allowance to pay for colour

printing.

Submission: Three copies of the fourth year project report must be submitted to

the Chairman of the Examiners, Honour School of [Engineering Science or Engineering,

Economics and Management], c/o Clerk of the Schools, Examination Schools, High Street,

Oxford, by noon on Friday of 4th week of Trinity Term 2011. This is a strict deadline

which must not be missed.

The report must not exceed 50 pages (including all diagrams, photographs,

references and appendices). All pages should be numbered, have margins of

not less than 20mm all round, and type face of Arial 11 point font with double

line-spacing. The report must be the candidate's own work and should include a signed

statement to this eect. A declaration of authorship form is attached for this purpose

and must be bound into the report after the title page, but need not be included in the

page count. Your risk and COSSH assessments must also be bound into the report, but

again need not be included in the page count.

Please also ensure that:

(i) your name and project title are on the report, but not your candidate number.

(ii) you have consulted the University's web site on plagiarism and how to avoid it:

http://www.admin.ox.ac.uk/epsc/plagiarism/index.shtml.
Finally, it is your responsibility to ensure that your work is handed in to the Exami-

nation Schools by the published deadline.

10
1.8.3 M.Sc.
Theses submitted by candidates in Engineering Science must not exceed 200 pages for

the Degree of M.Sc. (by research). They should be double spaced on A4 paper in normal

size type (Times New Roman, 12 point), the total to include all references, diagrams,

tables, appendices, etc.

For taught masters courses it can vary. The regulations for the Biomedical Engi-

neering (BME) Taught M.Sc. indicate a maximum of 60 pages. All pages should be
numbered, have margins of not less than 20mm round, and type face not less than 11 pt
font with line spacing of no less than 8mm. The spacing of 8mm (
1
3
mm) is generally

thought to be `double spaced'. The full regulations for this course can be found online

at:

http://www.admin.ox.ac.uk/examregs/17-40_SPECIAL_REGULATIONS.shtml#subtitle_
15)

1.8.4 PRS Transfer report

Transfer from Probationer Research Student PRS to M.Sc.(R) or D.Phil. status requires

the submission of a report and an oral examination. The details in this subsection

concerning this process are taken from the doc distributed by the Director of Graduate

Studies in 2010.

Every graduate student studying for a research degree in Engineering Science is re-

quired to register in the rst instance as a Probationary Research Student. During your

rst (research) year, you will receive an e-mail from the department informing you that

two academics will be appointed to join your supervisor(s) on a supervisory committee.

One of these will be a specialist in an area close to the topic of your research and the

other will be in a totally dierent eld. Towards the end of the rst year of research you

will submit a report to this committee and attend an oral examination to demonstrate

your ability to carry out work leading to the M.Sc.(R) or D.Phil. degree.

11
 In your report you will need to provide evidence that you have:

1. The necessary academic and other abilities to carry out original research of high

quality.

2. Suitable background knowledge through critical study of the literature.

3. An appropriate research topic likely to lead to a satisfactory thesis. This should

take 2 years for an M.Sc.(R) or 3 years for the D.Phil. from the start of your work

in Oxford.

4. The necessary resources for your research. Your supervisor will normally take re-

sponsibility with you for this.

If your written transfer report and your performance in the oral examination are sat-

isfactory, you will be sent a GSO.2 form, so that you may formally apply to the University
for change of status to M.Sc.(R) or D.Phil. student.

Your transfer report should cover much of your work in the rst nine months of your

research and be submitted to the Assistant to the Director of Graduate Studies not

later than eleven months after commencing graduate work in Oxford. For

the majority of students who start in Michaelmas Term, the submission deadline is 1st

September, for Hilary Term the submission deadline is 1st December and for Trinity

Term the submission deadline is 31st March.

The report should not exceed a maximum of 60 pages from front cover to last page

(including all diagrams, photographs, references and appendices). All pages should be

numbered, have margins of 20mm-30mm all round (ALL margins should be 20 mm-30

mm. The measurements taken are 20 mm - 30 mm from the top of the page to the top

of the rst sentence and likewise, from the bottom of the page to the bottom of the nal

sentence), type face of Times New Roman 12 font, and be in double-line spacing.

Reports that do not conform to these specications will not be accepted.

Before your report is printed and bound, it must rst be checked by the Departmental

Graduate Studies oce to ensure that it conforms to the regulations governing the correct

12
length and presentation. This can be done by e-mailing an electronic copy of your report

to: postgraduate.studies@eng.ox.ac.uk. Once it has been approved, your report can

then be submitted for printing by the print room. Reports which do not conform to the

regulations will need to be revised accordingly.

1.8.5 D.Phil.
The ocial rule in the Examination Decrees and Regulations (Grey Book) on thesis

length and presentation provides the following advice for D.Phil.:

The thesis must be typed or printed on one side of the paper only, with a margin of
1.25 to 1.5 inches (32 to 38mm) on the left-hand side of each page. Theses in typescript
should present the main text in double spacing with quotations and footnotes in single
spacing. In the case of word-processed or printed theses where the output resembles that
of a typewriter, double spacing should be taken to mean a distance of about 0.33 inch
or 8mm between successive lines of text. Where a word processor produces output which
imitates letterpress then the layout may be that of a well designed book. Candidates are
advised that it is their responsibility to ensure that the print for their thesis is of an
adequate denition and standard of legibility.
3
For good legibility you should use a 12 point font .

In addition to the rule in the Grey Book, see notes produced by the Graduate Studies

Oce Preparation and submission of thesis and abstracts submitted for the degrees of

D.Phil., M.Sc. (by research) and M.Litt. (ref. GSO1/Notes 2 Prep and Sub.). In

particular see 6. Regulations of Boards and Committees (xvii) Physical Sciences (b)

Word limits:

Theses submitted by candidates for the Degree of D.Phil in Engineering Science and
Physics (except Theoretical Physics) must not exceed 250 pages, A4 size, double spaced
in normal-size type (elite), the total to include all references, diagrams etc.
Some sub-departments (e.g. Physics) consider that 100 - 150 well-written pages should

3 http://www.physics.ox.ac.uk/PP/grad/GTC22.htm

13
 4
be sucient .

4 ibid

14
Chapter 2
Previous Work in the Field
2.1 Content of chapter 2
Chapter 1 should describe the physiology of the problem in much more detail, and perhaps

provide previous attempts to solve the problem you are addressing. This may wait until

Chapter 2 if it is particularly lengthy. Chapter 2 should include a through overview of

existing work in the eld. You need to show you are fully aware of previous work in this

(and related) areas, and are not simply repeating this work. Cite all relevant works, and

explain what they did and then later explain why what you are going to do either builds

on this, or that work is not relevant.

2.2 Chapter layout

Each chapter should be divided into sections and subsections using the commands \section,
\subsection and \subsubsection, forming a logical numbered hierarchy.

2.3 Internal (cross) referencing: the label command

Each section command should be followed by a label command (like \label{sec:crossref})
and referenced using the \ref command. for example, this section has been labelled with

15
the above label command, so we would reference it by using the command: \ref{sec:crossref})
which generates a number reference thus: 2.3.

2.3.1 Equations, tables and gures

Equations, tables and gures are referenced in the same manner as sections. That is, you

add a label (e.g. for an equation \label{eq:hyperbolic_orbit}) and then you cite it

like this:

As we can see from Eq. \ref{eq:hyperbolic_orbit},

the craft is out of control.

Latex will automatically generate the appropriate number (and link) for the \ref com-

mand and insert it after the abbreviation Eq.. Note that the equation is abbreviated.

This is not required, but you should just be consistent. Similarly, gure is abbreviated

to Fig. but table is usually kept as Table. Careful when referring to more than one

equation or gure!

2.3.2 Indexing
You can also index a given term using \index{term} and the makeindex command.

2.4 External referencing and bibliography

Note that when you cite a publication you will need to have a list of bibtex sources

for each citation and an associated tag. These are stored in your bible and are called

anything.bib (where anything can be ... well ... almost anything. In this template it is

imaginatively called refs.bib.

A typical bible will have an entry that looks like this:

@article{Tsiotou2005,
author = {Tsiotou, A. G. and Sakorafas, G. H. and Anagnostopoulos, G. and Bramis, J.},

16
journal = {Medical Science Monitor},
keywords = {Blood Coagulation Disorders, Systemic Inflammatory Response Syndrome},
mendeley-tags = {Sepsis},
month = {March},
number = {3},
pages = {RA76--85},
pmid = {15735579},
title = {Septic shock; current pathogenetic concepts from a clinical perspective},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15735579},
volume = {11},
year = {2005}
}

Don't be alarmed here - these can be generated automatically. Try something like

Jabref - http://jabref.sourceforge.net/ (see below). Notice that the reference begins

with @article and then an open curly brace. This tells bibtex that the rest of the text

to the nal closed curly brace refers to a journal article and so to format it accordingly.

The next item you will encounter is a tag that is specic to this particular reference - in

this case Tsiotou2005.

To cite an article like the one above, type \cite{Tsiotou2005} and a number (or

name and year) will appear in the brackets like this: [1]. In some versions of latex, the

PDF le will hyperlink this to the references at the end of the document.

Note, depending on the latex environment, you may have to run the bibtex command
separately to generate the bible, and then rerun the latex command twice to allow the

cross referencing to be picked up.

2.4.1 Automated reference search and generation: Jabref

Jabref (http://jabref.sourceforge.net/) is a powerful cross-platform bibliography

tool for managing your bib les (or databases). You can import and export multiple

17
formats, including Endnote. You can also do automatic searches and retrieve the bibtex

references, so you may never have to write one.

Jabref also supports searching within the references, including your own notes.

2.5 Figures
AT Xdocument using the
Chapter 1 illustrated how to insert a gure into a L E \includegraphics
AT Xtakes care of the positioning for you, but you can tell it your preferences.
command. L E

After the \begin{figure} command, you can add a location order preference in square

braces. The locations are:

ˆ t - top of the page

ˆ b - bottom of the page

ˆ p - on the next page

ˆ h - here, at this point in the text

So, if you write \begin{figure}[tbp] AT Xwill attempt to place the gure at the top
L E

of the page. If there is no space, then it will try to the bottom, then the next page, and

sometimes later pages.

2.5.1 Labels, Legends, Units and Captions

Each gure should have all axes labelled with the correct variable (used in the text),

followed by the units in braces.

E.g.: Arterial Blood Pressure (mmHg)

Make sure the font is large enough to read. If you add a legend, make sure the same

principles hold.

Each gure must have a caption below it, which is basically self-contained and de-

scribes the gure contents, including all variables plotted, and what the reader should be

18
looking for - i.e. the point you are trying to make. Do not put a title on the gure (like

you do in Matlab), since the caption should contain all the descriptive langauge.

Do not write something like `see text for details'. This is a pointless statement.

Obviously the text contains the details, but the reader should be able to understand the

gure by reading the caption. Of course, the caption is just a summary and should not

repeat the text, and should not generally grow to take up more than 34 lines at most.

2.5.2 Figure format

It is wise to save your gures in several formats so that you can use them in many

dierent media (PPT, HTML, PDF, etc). The best formats are PNG, (lossless) JPEG,

PDF, EPS and Matlab's native FIG format. The PNG and PDF are useful when you

compile directly to PDF. The EPS format is useful when compiling direct to postscript.

The FIG format is useful (assuming you are using Matlab) because it saves all the data

used to generate the gure, and allows easy manipulation of the fonts, zoom, axes etc

after the fact. Your supervisor / external examiner will require such adjustments, so you

want to make sure you save the raw data

One of my colleagues was asked by her external examiner to increase the font size on

every gure in her thesis. That meant re-running every single experiment in her D.Phil!

2.5.3 Combining gures

You can also scale images, and stack multiple images in a gure, as in Fig. 2.1. Note the

AT Xsource.
reference label is placed inside the caption in the L E

2.5.4 Common gure mistakes

Let's look at Figure 2.1. What can you see wrong with it?

ˆ The data types are in colour, but not distinct shapes. When you print this in

black and white, (or if you have a slight colour blindness) then the plot will become

19
 Figure 2.1: Combining several plots into one

(a) 15 min segments, slid by 3 min with 1 (b) 15 min segments, slid by 3 min with 5

min anchor windows min anchor windows

(c) 30 min segments, slid by 5 min with 1 (d) 30 min segments, slid by 5 min with 5

min anchor windows min anchor windows

20
 meaningless. Assume black and white printing.

ˆ The caption is too terse. It doesn't describe the gures well.

ˆ None of the abbreviations are dened in the caption.

ˆ There are no units on the axes (in parentheses after the parameters).

ˆ The numbers on the axes and the parameter labels are far too small.

ˆ The Matlab gures still have their titles - these should be removed and all informa-

tion be provided in the caption.

ˆ The presentation of the data is misleading. The scales are dierent on each graph,

so comparisons cannot be made.

What's right with it?

ˆ The data types are at least consistent between graphs. It's important that if colours

are used, then they mean the same thing from graph to graph.

ˆ Each subplot is labelled a, b, c, d .... you should never say 'the upper plot' or the

left plot.

On this latter point, be aware that you should never make statements about the gure

which refer to its position in the text. It can move around, and so will your text as you

expand and edit. For example, the phrase 'in the gure below' is not acceptable. When

you do refer to the gure, make sure you use the \ref{} command and the same name

used in the \label{} command in the caption.

Finally: always make sure you have referenced every gure at least once. Never leave

a gure hanging in the document without a good reason for it being there and a full

explanation of its contents. To check, just search (using the command line tool `grep' for

example) through all your TeX les for the number of times a label is used. (Also check

that there is a label in every caption.)

21
2.6 Tables
Tables are treated like gures, except that they are pure text, and are numbered sepa-

rately. Note that all terms in a table, as for gures, need to be dened in the caption

if they were not already in the text. Symbols (such as † to indicate signicance) should

also be dened.

An example of a complex table is given in Table 2.1.

Table 2.1: Variable Boundaries for physiological parameters used in this study.

Variable Medical Bounds Data Deviation Bounds

ABPMean 10 - 220 16.74 - 143.79

ABPSys 30 - 250 19.78 - 210.74
ABPDias 10 - 200 5.53 - 117.78
CVP 0 - 50* -348.81 - 404.01
HR 10 - 220 21.43 - 153.93
RESP 0 - 70 -171.59 - 209.54
SpO2 50 - 100 69.02 - 124.21
PULSE 10 - 220 8.02 - 161.51
NBPMean 10 - 220 31.40 - 117.36
NBPSys 30 - 250 41.80 - 171.03
NBPDias 10 - 200 17.94 - 112.16
PAPMean 5 - 100* -12.07 - 75.82
PAPSys 5 - 100* -15.65 - 106.71
PAPDias 5 - 100* -9.95 - 57.51

2.7 Equations
AT Xseems fairly natural after a short period of time.
Equation writing in L There are
E

essentially three ways to place equations into your thesis.

2.7.1 In-line equations

The rst is in-line like this: an = b n + c n , where a is the number of apples, b the number

of bananas, c the number of cakes, and n is a prime number. Note that all terms are

dened directly before or after the rst time they are used.

22
 The above equation is generated with the text $a^n = b^n + c^n$. Note that the

dollar sign starts and ends the math environment in-line.

Note also that in-line equations are not numbered. So if you ever want to refer back

to an equation, do not make it in-line.

A full list of symbols you might use in equations can be found in David Carlisle's

1
symbols.tex le . or here:

http://web.ift.uib.no/Teori/KURS/WRK/TeX/symALL.html.

2.7.2 Numbered equations

Numbered equations can be generated in this manner:

\begin{equation}
\cos 2\theta & = & \cos^2 \theta - \sin^2 \theta
\label{eq:trig}
\end{equation}

which creates equation 2.1 as follows:

cos 2θ = cos2 θ − sin2 θ (2.1)

Note the position of the label inside the equation environment. You can refer to an

equation using the \ref{} command.

2.7.3 Equation arrays

Sometimes, you want to make arrays of equations, but not number every line, such as

when you are listing derivations. To do this you can do the following:

\begin{eqnarray}
(\frac{1}{N})^2 \cos 2\theta & = & \frac{1}{N^2} \cos^2 \theta - \sin^2 \theta \\ \non
1 http://web.ift.uib.no/Teori/KURS/WRK/TeX/latexsource.html

23
\cos 2\theta & = & \cos^2 \theta - \sin^2 \theta \\ \nonumber
& = & 2 \cos^2 \theta - 1.
\end{eqnarray}

Note that the = symbol is bordered by an ampersand, so we have made a table,

aligned around this symbol.

The above code gives:

1 2 1
( ) cos 2θ = cos2 θ − sin2 θ (2.2)
N N2
cos 2θ = cos2 θ − sin2 θ

= 2 cos2 θ − 1.

Or you can be more complex:

   
 1 1   (ζ − z) − (ζ − z − h) 
 ζ − z − h − ζ − z  =  (ζ − z − h)(ζ − z) 
   
 
 h 
=  
(ζ − z − h)(ζ − z) 
2|h|
≤ .
|ζ − z|2

The asterisk in eqnarray* suppresses the automatic equation numbering produced by

AT X. This is not required of course, and you can just use

L E \nonumber at the end of any

line you do not want numbered.

2.8 Footnotes
footnotes are generally for you to insert in passing information that may be pertinent,

2
but distracts the reader from the main argument . Use sparingly and try not to make

2 Just like this sentence, which is an example of how you generate a footnote.

24
them lengthy.

One place where you perhaps should use footnotes is in the introduction to a chapter

when you introduce the work you are about to present. If it has been published, or is

in preparation, insert a footnote explaining this, and giving the exact reference. This

helps the examiner know if anyone else has veried that section of the thesis. Note that

the reference will be repeated at the end of the thesis too in section B. Don't make the

examiner ick backwards and forwards too much!

2.9 Appendices
These are like large footnotes. Large data tables or long derivations can go in an appendix.

2.10 Abbreviations
Abbreviations should be dened the rst time you use them, and then subsequently you

should stick to the abbreviated form. (Since an abstract is self contained, abbreviations

must be dened therein and again in the main text.) Do not abbreviate a term you use

only once. A list of abbreviations in an appendix is useful.

2.11 Glossary
A glossary of technical terms (particularly from a related eld such as physiology) can

be useful.

2.12 Symbol list

If your thesis contains a lot of mathematics it is useful to have a list of variables in an

appendix with exactly what each one means. This is particularly important if you use

the same parameters from chapter to chapter.

25
 This is also a good exercise to help you identify where you have dened your variables

and if you have used more than one symbol for the same variable, or one symbol for

several variables.

26
Chapter 3
Data Used in Thesis and Preprocessing
In this chapter you should include a detailed description of all the relevant public data

sets available, and justify why you did or did not use them. Then describe what data

you collected and why. Also include any steps you took to remove 'erroneous' data and

justify their removal. Preprocessing steps must also be detailed.

3.1 Plagiarism and collusion

Durham University has a good denition of plagiarism and collusion: Plagiarism: unac-

knowledged quotations or close paraphrasing of other people's writing, amounting to the

presentation of other person's thoughts or writings as one's own. This includes material

which is available on the world-wide web and in any other electronic form.

This also includes algorithms and computer code, even if you are translating them into

another language. Of course, some algorithms are so standard (such as the FFT) that

they do not require citation, although the specic implementation does require credit.

From my point of view, this is just good scientic practice, since not all FFTs are the

same. It's important that the algorithm has been benchmarked and the specic version

is noted in case bugs are found later which invalidate or weaken your conclusions.

Durham University's denition of collusion is as follows: Collusion: working with

27
one or more other students to produce work which is then presented as one's own in a

situation in which this is inappropriate or not permitted and/or without acknowledging

the collaboration. Neither is acceptable. Even if you are working in teams, you must

describe who did what - see 'authorship' below.

3.2 Authorship
Many journals do not even specify what constitutes authorship on a scientic article. I

think the Authors' contributions section of Biomedical Engineering Online provides an

excellent description: An `author' is generally considered to be someone who has made

substantive intellectual contributions to a published study. To qualify as an author one

should 1) have made substantial contributions to conception and design, or acquisition

of data, or analysis and interpretation of data; 2) have been involved in drafting the

manuscript or revising it critically for important intellectual content; and 3) have given

nal approval of the version to be published. Each author should have participated suf-

ciently in the work to take public responsibility for appropriate portions of the content.

Acquisition of funding, collection of data, or general supervision of the research group,

alone, does not justify authorship.

All contributors who do not meet the criteria for authorship should be listed in an

acknowledgments section. Examples of those who might be acknowledged include a per-

son who provided purely technical help, writing assistance, or a department chair who

provided only general support. List the source(s) of funding for the study, for each au-

thor, and for the manuscript preparation in the acknowledgments section. Authors must

describe the role of the funding body, if any, in study design; in the collection, analysis,

and interpretation of data; in the writing of the manuscript; and in the decision to submit

the manuscript for publication.

Dierent elds consider the subject of authorship in dierent manners though. Clin-

ical publications often carry authors who `just' collected the data to provide sucient

28
credit for the enormous eort this involves. You will probably be expected to co-author

with other researchers and academic or clinical sta. Unless the article is in a completely

unrelated discipline, you will be expected to pass all potential publications through your

supervisor before presenting in public, placing on any website, submitting to a jour-

nal/conference/workshop etc, or presenting/publishing in any public way (including at

college or group meetings). This is to protect the professional reputations of all involved.

If you wish to claim sole authorship of a work (such as an article or patent), this can be

considered by your supervisor in the rst instance, and then if there is a disagreement,

by the IBME academic sta.

There is one caveat here. If you do not answer emails in a reasonable period of time

(or leave a forwarding email), your supervisor may choose to publish some of your work

without your agreement. This is to ensure that research progresses despite your omission.

3.3 Acknowledgments and funding bodies

The following is from Biomedical Engineering Online's instructions for authors: Anyone

who contributed towards the study by making substantial contributions to conception,

design, acquisition of data, or analysis and interpretation of data, or who was involved

in drafting the manuscript or revising it critically for important intellectual content, but

who does not meet the criteria for authorship should be named in an acknowledgments

section. Please also include their source(s) of funding. Please also acknowledge anyone

who contributed materials essential for the study. The role of a medical writer must be

included in the acknowledgments section, including their source(s) of funding. Authors

should obtain permission to acknowledge from all those mentioned in the Acknowledg-

ments.

29
3.4 References, citations and `personal communications'
It is important that all (key) relevant materials are cited in your publication. This

includes anyone who's work you have used, and any work you have considered but rejected.

When citing the work you should be careful to indicate why you have used or rejected

the material. Note that if the source you cite is not primary, you need to cite the

primary source as well (or instead). Note, you cannot cite a paper to justify or explain a

technique which does little more than cite another paper to justify or explain a technique.

It is important that the format of the references remains consistent. Although some

journals require the Harvard style, I prefer Vancouver. The following is from Biomedical

Engineering Online's instructions for authors (and is the Vancouver style):

All references must be numbered consecutively, in square brackets, in the order in

which they are cited in the text, followed by any in tables or legends. Reference citations

should not appear in titles or headings. Each reference must have an individual refer-

ence number. Avoid excessive referencing. Only articles and abstracts that have been

published or are in press, or are available through public e-print/preprint servers, may

be cited; unpublished abstracts, unpublished data and personal communications should

not be included in the reference list, but may be included in the text. Obtaining permis-

sion to quote personal communications and unpublished data from the cited author(s) is

the responsibility of the author. Journal abbreviations follow Index Medicus/MEDLINE.

Citations in the reference list should contain all named authors, regardless of how many

there are. Web links and URLs should be included in the reference list. They should be

provided in full, including both the title of the site and the URL, an author (if known)

and the date accessed (since the web is ephemeral). Note that a thesis can be consid-

ered a peer-reviewed publication to cite, but it is of little use if the thesis is not readily

available. If a paper exists, it is best to cite that instead (or as well), or if the thesis is

publicly available, then a URL can be provided.

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3.5 IRB/Ethics approval
If your work involved living subjects other than yourself, you (or whoever collected the

data) must have obtained ethical approval for the study. Again, BMEO's policy provides

an excellent guide: Any experimental research that is reported in the manuscript must

have been performed with the approval of an appropriate ethics committee. Research

carried out on humans must be in compliance with the Helsinki Declaration, and any

experimental research on animals must follow internationally recognized guidelines. A

statement to this eect must appear in the Methods section of the manuscript, including

the name of the body which gave approval, with a reference number where appropriate.

Informed consent must also be documented. Manuscripts may be rejected if the editorial

oce considers that the research has not been carried out within an ethical framework,

e.g. if the severity of the experimental procedure is not justied by the value of the

knowledge gained. The practice of explicitly stating which ethical body approved your

study is often not followed in engineering journals, but never-the-less you should ensure

it exists.

In the UK, you must le an ethics approval through `IRAS', which is a national stan-

dardised submission system. Sometimes waivers are granted by your instituion, based on

the fact that other ethics review committees have approved the study you are perform-

ing. Always check with your institution's ethical review body. In the United States, the

ethics review body is known as the 'Institutional Review Board', or IRB. IRB approval

is equivalent to ethics approval. Most research institutions have their own IRB.

The exception to the above guidance is if the data has been posted publicly (and

hence de-identied - see HIPAA rules for example) such as on PhysioNet. In such cases,

data can generally be freely used without ethical approval. Some countries may not agree

with this of course. Check local rules in both your country and the country of origin of

the data to be sure, and follow the most stringent of rules. Just because a country does

not require strong ethical approval does not mean you are exempt from your local rules.

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3.6 Double publishing
Any manuscripts submitted to a journal must not already have been published in an-

other journal or be under consideration by any other journal, although it may have been

deposited on a preprint server. Manuscripts must not have already been published in any

journal or other citable form, with the exception that the journal is willing to consider

peer-reviewing manuscripts that are translations of articles originally published in an-

other language. In this case, the consent of the journal in which the article was originally

published must be obtained and the fact that the article has already been published must

be made clear on submission and stated in the abstract. Manuscripts that are derived

from papers presented at conferences can be submitted unless they have been published

as part of the conference proceedings in a peer reviewed journal. Authors are required to

ensure that no material submitted as part of a manuscript infringes existing copyrights,

or the rights of a third party. You can take concepts from previous articles and develop

them, or write expanded versions of conference articles in some journals. It varies from

journal to journal and eld to eld. Medical journals, although much more relaxed on

authorship, generally don't allow you to publish any concept (in an expanded form or

otherwise) that has previously been published or presented at a conference.

3.7 Copyright
See Cal Tech's resource for denitions and a discussion on how much you can borrow

before you are infringing on copyright. For example, you can photocopy or print a

certain percentage of many copyrighted journals or books for personal or teaching use.

Some journals require you sign over your copyright to them. I would discourage this

practice. See the webcast of Hal Abelson (from MIT) for a good justication on why we

should not trade our IP for relatively low up-front publishing costs. Other journals, such

as BioMedical Engineering OnLine allow authors to retain copyright to their work for a

slightly higher up-front publishing fee. Access then is free, and you are more likely to be

32
cited. (Three times as much at the last count.)

3.8 Conicts of interest

The university of Oxford states: A conict of interest arises where the commitments

and obligations owed by an individual member of sta or student to the University or to

other bodies, for example a funding body, are likely to be compromised, or may appear

to be compromised, by:

ˆ that person's personal gain, or gain to immediate family (or a person with whom

the person has a close personal relationship), whether nancial or otherwise; or

ˆ the commitments and obligations that person owes to another person or body.

There can be situations in which the appearance of conict of interest is present even

when no conict actually exists. Thus it is important for all sta and students when

evaluating a potential conict of interest to consider how it might be perceived by others.

The duty to declare a possible conict applies to the perception of the situation rather

than the actual existence of a conict. However, the duty is not infringed if the situation

cannot reasonably be regarded as likely to give rise to a conict of interest. Conicts

of interest may be nancial or non-nancial or both. Further information about both

types of conict and Oxford University's conict of interest policy can be found here:

http://www.admin.ox.ac.uk/rso/integrity/conflict_interest_policy.shtml.
Basically, if you know someone involved in a project that you could inuence or could

inuence you, or if a relative or friend is nancially connected with your research or

publication, you need to declare this. It doesn't invalidate the study but not declaring

this, may cast signicant suspicion on the research at a later date. Not declaring interests

may even lead to your employment or course of study being terminated, amongst other

repercussions.

33
3.9 Patents
Patents are designed as a reward for publicly disclosing an invention from which every-

one can benet (particularly when the patent period ends). The incentive for this public

disclosure is a limited period of protection from competition. Patents also provide in-

centives for investors to back research and companies that translate the research into a

practical product. As far as I am aware, nothing stops you from developing research using

patented material, in the same way you can use any published material - you just can't

make money from it, or let others use it, unless the patents are licensed. However, patents

can limit from where you can receive funding (because of conicts of interest). Patenting

an idea may also disincentivize others to work in this area, diminishing the impact of

your research. It's also an expensive and time consuming process unless someone else is

willing to do all the leg work for you (which is unlikely).

3.10 Source code and open source

Most code you nd online will carry a license with it. If it doesn't, it probably isn't

free and you shouldn't use it. It's hard to cite it, but it still isn't yours. Licenses vary

in the extent to which you can use, copy or embed them in other code, and often their

licenses require you to inherit their licenses (`copyleft'). As Richard Stallman will tell

you, 'free' doesn't mean free as in beer, it means liberated, as in open to scrutiny, which

is what science should be. You can copyright your code, and license it to third parties,

retaining extensive rights for yourself and others. You can even patent code. If you work

in my research group, your code will probably inherit an open source license and end up

in the public domain. If you are unhappy with this idea, let me know up front. (N.B.

You can still patent the idea for which you have released open source code! If it is after

you publicly released the code, then only in the US - where you have 12 months to le a

provisional or full patent.) If you are confused about which free software license to use

(and have the liberty to choose), please see this quick look-up chart:

34
http://en.wikipedia.org/wiki/Comparison_of_free_software_licenses

3.11 Presentations, conferences and other `publications'

Any presentation outside of a internal group meeting (not attended by non-Oxford re-

searchers) should be considered `public'. This means you are presenting our research (not
just yours) and so you should send your supervisor your material intended for publication

(e.g. slides) well in advance (noting any other contributors prominently in the material).

Your research reects the input of your collaborators and so they should be aware of it

in advance, and be given the chance to correct errors or contradictions. You rarely work

alone!

3.12 Sharing results before publication

You should talk to your supervisors before sharing research and results with other groups.

Generally most people like to share and work in an `open' manner, but sometimes this can

be sensitive. However, you may nd that your supervisor shares your research with select

colleagues without discussing this with you rst. (They should not have to pre-approve

every communication they have with colleagues with you.)

Well - I hope that covers it. Feel free to drop by and discuss this with me. If you see

me stray from these guidelines, please do call me out - no-one is perfect!

3.13 Disclaimer
I'm not a lawyer, and much of the information on in this document might be wrong,

particularly in dierent regions. Laws change, interpretations change and precedents are

set. So none of the information in this document should be used without consulting

a lawyer and all appropriate authorities. Do your own research as well as reading the

35
research and thoughts of others. Note also that the rules change over time, so check the

university admin pages for the most up to date information.

36
Chapter 4
Clever things I did to the data part 1
Main research - part 1.

37
Chapter 5
Clever things I did to the data part 2
Main research - part 2.

38
Chapter 6
Clever things I did to the data part 3
Main research - part 3. There might also be more parts ...

39
Chapter 7
Conclusions and future work
This chapter should summarise your results, interpretations and conclusions. Highlight

your exact contributions. Discuss limitations and suggest future work.

40
Appendix A
Timeline for completion

41
 This section is for your PRS transfer report only. It should include a gant chart

detailing your taks and time-line to comlplete the thesis. Delete this chapter for all other

reports.

There is a spread sheet you can use to create your own Gantt chart, supplied with

this template, probably called:

ThesisGanttChart.xls

or

ThesisGanttChart.odt

To insert the chart you'll need to covert it to an image and insert it as a gure. Any

other Gantt chart format is ne - even a simple table.

Note that you will need to edit it yourself and insert all the elements of your future

proposed work. Don't make it too general, like i) Collect Data, ii) Analyze Data, iii)

Write up. This will be laughed out and you'll have to rework your report. List the

dierent experiments you intend to do with realistic time lines. Build in time for writing

and submitting the thesis and assocaited papers (as separate items) too.

42
Appendix B
List of publications and presentations

43
 Do not include this section for your short summer project.

Otherwise, this section should contain a chronological list of publications that are in

preparation, in submission or have been published if any at all. Note into which category

each publication falls indicate if the journal or conference is peer-reviewed.

Make sure you indicate as a footnote, where research in a chapter has been published,

or is in submission. This helps the examiner know if anyone else has veried that section

of the thesis.

Also include a list of any presentations you have given, unless included as a conference

paper above.

For the PRS transfer report, include a list of courses and relevant lectures attended.

44
Appendix C
Abbreviations and glossary of terms

45
 List all your abbreviations alphabetically here. Also, for clarity and since the nature

of your thesis is cross-disciplinary yet highly specic, a glossary of clinical terms, technical

abbreviations and explanations of contextual descriptors should be provided.

Be sure to cite from where you drew the denitions.

C.1 Abbreviations
ˆ ABP: Arterial Blood Pressure - a general term for the systemic arterial blood pres-

sure. Measured in units of mmHg either invasively or using an inatable cu,

usually in/on the arm or thigh.

ˆ ECG: Electrocardiogram - a time series of electropoential dierences between two

points on teh upper body, indicative of cardiac electrical activity. Measured in mV,

and usually sampled at 250Hz, 12 bits, or greater.

C.2 Glossary
ˆ Adventiita  Membranous structure, usually morbid, covering but not belonging to

an organ.

ˆ Aerent Nerves  Carry impulses to the muscle/gland/organ.

ˆ Angiotensin  A powerful vascoconstricting polypeptide which stimulates the pro-

duction of aldosterone and vasopressin and results in an increase in blood pressure

(more fully angiotensin II); angiotensin I, the inactive precursor of this, which is

formed in the liver by the action of renin on a plasma protein (angiotensinogen),

and is converted in the lungs to angiotensin II by a second enzyme.

ˆ Aortic stenosis  progressive narrowing of the aortic valve resulting in the obstructed

passage of blood from the left ventricle into the aorta. Chronic stenosis can lead to

left ventricular enlargement and congestive heart failure.

46
ˆ Arrhythmia  Any variation from the normal (sinus) rhythm of the heart beat,

including preamture beats, heart block, atrial brillation and atrial utter.

ˆ Artefact (Sometimes Artifact)  a product or eect that is not present in the natural

state (of an organism, etc.) but occurs during or as a result of investigation or is

brought about by some extraneous agency such as electrode movement.

ˆ etc ...

47
Bibliography
[1] Adelais G Tsiotou, George H Sakorafas, George Anagnostopoulos, and John Bramis.

Septic shock; current pathogenetic concepts from a clinical perspective. Medical sci-
ence monitor : international medical journal of experimental and clinical research,
11(3):RA7685, March 2005.

48