What’s going on at the UOC?

Q. What has Mars, Epidemics, Heart Disease, Infection, and Pacifika got in common?

A. They are all central to research project at the University of Otago Christchurch (UOC).

Here are some excerpts for the UOC summer newsletter (Written by UOC communications manager, Kim Thomas).

Christchurch in NASA Mars project role

University of Otago, Christchurch, researchers are playing a crucial role in research that will assist in NASA’s mission to Mars.

Screen Shot 2016-02-09 at 10.15.21Thee Christchurch researchers are scanning the brains of explorers who have wintered in Antarctica as part of a NASA /German Aerospace Center project to understand what impact living in extreme environments has on the human brain. The research will be relevant for NASA’s plans to send humans to Mars. The shortest possible return trip to the red planet would take two years.

The international research team is led by the University of Pennsylvania’s Associate Professor Mathias Basner. His team will be scanning the brains of astronauts, while the Canterbury team focuses on those who have wintered in Antarctic’s extreme and isolated environment.

Dr Tracy Melzer is the MRI research manager for the Christchurch campus’ New Zealand Brain Research Institute. He says the research aims to understand whether prolonged periods in these extreme, isolated and hostile environments change brain structure and function.

His international collaborators have already found the hippocampus region of the brain, which is important for memory formation and visual/spatial orientation, actually shrinks during the Antarctica winter.

Dr Melzer and his colleagues will scan the brains of up to 28 international explorers over two years. They are tested before leaving for Antarctica, immediately on their return, then six months afterwards. The Christchurch scans are important because they capture explorers immediately as they return from the ice.

Preparing for future disease epidemics

Christchurch microbiologist Professor David Murdoch has taken part in an invitation-only global think tank aimed at better anticipating future infectious disease epidemics.

The head of the University of Otago, Christchurch’s Pathology Department was one of two Australasians invited to the World Health Organization-led event late last year.

Professor Murdoch says he was privileged to be among about 130 international experts invited to attend, including human and animal health experts, and members of aid agencies and the insurance and travel industries.

“ The big idea was how to better prepare for future epidemics, knowing there definitely will be ones. It also recognized reviews of the Ebola response and a desire to improve on that.”

Acknowledging the importance of collaboration, one key outcome of the event was getting people from diverse areas of expertise together, Professor Murdoch says.

Thee event consisted of six sessions, including ‘Back to the future: learning from the past’, and ‘Preventing the spread of infectious disease in a global village’. Each session consisted of short talks by five experts, then robust discussion.

Professor Murdoch spoke at the event about the relatively new area of microbiomes (the communities of microorganisms that inhabit parts of the human body) and how understanding it could help with preparing for and controlling future respiratory disease epidemics.

Some of the ideas that emerged from the event were that global and public health were getting more political attention than ever, and that health threats increasingly reflected nature, including the animal world, and so acknowledging and understanding its interplay with human health was important.

Contact between children monitored in world first infection study

Christchurch primary school pupils are wearing sensors tracking contact with each other in a world-leading study to better understand a common but serious disease.

The staphylococcus bacterium is a major cause of serious infections such as septicaemia, but also often presents as sores on the skin. Most commonly, though, it is carried harmlessly on skin or in noses, from where it can be passed on to others who might become ill. Very little is known about who passes it to whom in the community.

University of Otago, Christchurch researcher Dr Pippa Scott is testing levels of the bacteria in Linwood Avenue School pupils and, in a world first, monitoring contact between them using ‘proximity sensors’ to better understand how staphylococcus is passed from person to person.

Dr Scott says school-aged children o en spread u and other diseases so could be important to the spread of staphylococcus in the community.

“We asked a lot of schools if they would take part in the study and Linwood Avenue School principal Gerard Direen came back to us quickly and said the school would be really keen to help.’’

Dr Scott says 70 children aged between 8 and 11 were given the proximity sensors to wear clipped to their shirts for around 2 weeks. e sensors are not GPS devices and cannot pinpoint a child’s whereabouts but rather record when children come in contact with each other. They have never before been successfully used in a study linking infectious disease spread to contact in the same individuals.

The study is ongoing but early analysis found almost every child was carrying the bacterium at some stage during the seven times they were tested. More than half the children carried the bacteria at any one test session. Almost all strains the children had were susceptible to commonly prescribed drugs for the condition.

First study of South Island Pasifika heart health

“She was one of the first scientists to demonstrate our cells produce free radicals as part of their normal function.”

It’s well known that New Zealand’s Pacific population suffers higher rates of heart disease than the general population. But until now, evidence has been based on data gathered
in Auckland. University of Otago, Christchurch researcher Dr Allamanda Faatoese is changing that with the launch of the Pasifika Heart study of Christchurch Pacific people.

“Pacific communities living in Auckland have vastly di erence environments than those in Christchurch. We know little about the heart health pro le of Pasifika people in Christchurch,’’ she says.

The Heart Foundation-funded Pasifika Heart study will for the first time measure heart disease risk factors in 200 Pacific Island participants, both healthy people and those su ering from illness. Dr Faatoese is based at the University’s Christchurch Heart Institute but will study participants from across the South Island.

Each participant’s personal and family medical history, blood pressure and body composition will be recorded along with their cholesterol levels, blood sugars and markers linked with kidney function, gout and heart failure.

(c) Creative Commons. Intangible Arts https://www.flickr.com/photos/intangible/

The physics of maiming a child (repost because of another close encounter)

Dear Driver,

When you backed out of a driveway and did not even see how I swerved around behind your car to avoid T-boning you, how dare you have the temerity to tell me you were careful!  I was 7 feet tall, dressed in bright yellow and traveling at no more than 10 km/h.  Perhaps a simple lesson in physics will help you and your fellow “driveway backers” to realise how dangerous you are and to adopt safer driving practices.

In the diagram you can see a car backing out of a driveway.  Typically when you are at the edge of your property and have a fence (see photo below) blocking your view of the footpath you are able to see about 1.7 metres along the footpath.  Let us imagine that there is a child on a trike riding at 5 km/h just out of your line of sight.  How long  does it take them to travel that 1.67 metres?  The physics is quite easy.

Car backing out of a driveway. Illustration of how little of the footpath can be observed.

Car backing out of a driveway. Illustration of how little of the footpath can be observed.

Velocity = distance/time, therefore time = distance/Velocity.

5 km/h is 5000 metres in 60 x 60 seconds, ie about 1.4 m/s.  Putting this in the formula above means that it takes about 1.2 seconds for the child to travel that 1.67 metres.

Now consider this. According to design guidelines for safe bicycle use 2.5 seconds must be allowed for someone to observe the danger, react, apply brakes and stop.  In other words, if you covered the distance from your driveway to the middle of the footpath, about 1 metre, in under 1.2 seconds you will almost certainly hit the child.  That is a speed of just 3 km/h!!!!!

Now consider who else is on the footpath, all legally:

  • Pedestrians 5 km/h
  • Joggers 5- 15 km/h
  • Kids on skateboards or scooters 10 km/h
  • Child on bicycle with small wheels, 10 km/h
  • Mobility scooter, 5-10 km/h
  • Me on my Trikke, 10 km/h
  • Postie on a bike 5-10 km/h.

For those going 10 km/h your speed needs to be just over 1.5 km/h to hit someone!

So, before you do some damage here is what you can do:

  • Never back out of a driveway unless you really really must.  If you think you must because of the design of your driveway, change the design!
  • Cut back those hedges, remove some of that fence so that you can see further.
  • Always always always stop at the end of your driveway (BEFORE THE FOOTPATH) and toot a horn.  Then proceed very very slowly.

By the way, you are legally obliged to give way:

 Land Transport (Road User) Rule 2004

4.4 Giving way when entering or exiting driveway

A driver entering or exiting a driveway must give way to a road user on a footpath, cycle path, or shared path (as described by clause 11.1A(1)).

Thank you for considering the physics of maiming a child, may you never find your self in such a terrible situation.


Dr John Pickering

A typical driveway with almost non-existant visibility

A typical driveway with almost non-existent visibility


Feature Image: Intangible Arts https://www.flickr.com/photos/intangible/ under Creative Commons Attribution 2.0 licence.

Self plagiarism – a misnomer

The story so far…

Dr Jaimi Whyte publishes in the NZ Herald an article that portions of which are substantially similar to an article he published in Britain in 2005.  This was picked up somehow by @LI_politico who posted:

Twitter on Jaimi Whyte


The NZ Herald subsequently asked Dr Whyte for his reaction to the accusation of self-plagiarism & reported that he did not see anything wrong with submitting an article which was a variant of one he had already published and [besides] Dr Whyte added “There’s clearly no such thing as self-plagiarism.”

I tweeted the article in reaction to the statement about self-plagiarism saying that I agree with Dr Whyte.  This resulted in some very interesting twitter discussion with a number of academics including   .  There were a number of good points made about whether this was more a case which should concern a possible breach of copyright (Dr Whyte had originally published his views in a book; I am not sure who owns the copyright) or whether it was a case of plagiarism; and also about why Dr Whyte’s action may be wrong.

My initial point was that Dr Whyte’s action was not plagiarism. I made this because when I was asked to write an encyclopaedia article on plagiarism a few years back I found that the generally excepted definition was “To represent oneself as the author of some work that is in fact the work of someone else.”[1]  Critically, it is only plagiarism if it is someone else’s work that is being “passed off” as one’s own.  This, though, is not necessarily a universal definition.  pointed to a University of Calgary definition of self-plagiarism:

“Self-plagiarism, however, must be carefully distinguished from the recycling of one’s work that to a greater or lesser extent everyone legitimately does. … Among established academics self-plagiarism is a problem when essentially the same article or book is submitted on more than one occasion to gain additional salary increments or for purpose of promotion.

Like all plagiarism the essence of self-plagiarism is the author attempts to deceive the reader…”[2]

I don’t think Dr Whyte’s article in the NZ Herald would meet the the University of Calgary’s strict definition of self-plagiarism as there is no hint of publication to enhance promotion aspects.  Dr Whyte, is a former politician.   “Repeating oneself” as a politician has become an art form – infuriating in the extreme during election season when we only hear the same thing over and over again.  The angst within academia appears to be that if one repeats oneself in order to gain advantage (eg prestige, promotion etc), then that is deception and not to be done.  On the other hand, as academics we are required to promote what we discover and think (in NZ law to be the “critic and conscience of society”).  Where that comment is confined to the academic journals where we could self-cite (sometimes frowned upon) an issue of deception by replication may be easy to spot.  However, as academics increasingly make use of new media, much of which is not limited to academics, as a means to engage, discuss, debate, and pontificate the line between deception and merely conforming to the norms of the media – ie where citation is not the norm & self-citation may be seen as arrogance and loose one’s audience  – becomes blurry.

The cop-out on many a publication where the results of the experiment are somewhat equivocal is to write “Further study is needed.” [guilty as charged… but only when referees push for this kind of comment].  Certainly here, further discussion is needed.  If you do engage in such discussion, perhaps consider also that the context of plagiarism is culturally bound:

“Plagiarism in the West rests on the assumptions that individuals can and do own their own words and content. …In many non-Western cultures, people find value in their relationships and position in society rather than in their expression of self. In such collectivist cultures, plagiarism is not recognized as a social wrong.”[1]


[1] Pickering, J. W. (2008). Plagiarism. In V. N. Parillo (Ed.), Encyclopedia of Social Problems (pp. 664–667). SAGE Publications: Thousand Oaks, USA.

[2] http://people.ucalgary.ca/~hexham/content/articles/plague-of-plagiarism.html#types



Downtown Toms River.  Source: Wikipedia

Toms River

TomsRiverToms River is a mystery. Not a mystery about the missing apostrophe, though that does warrant a thorough investigation. Rather, Toms River is a forensic mystery, an intrigue of science and health, of the marvels of chemical manufacturer and of the mischievousness of chemical pollution, and finally of that old conundrum of correlation verse causation. The writing flows like that of a well written novel – good enough that one forgets at times that it is not fiction, but a story about real people and real events. At the nub of the mystery is that so human of all questions, “why?” Why does my son have cancer? The answer provided in Toms River is neither sensational nor simplistic. To try and get near an answer the author must explore the histories of dye manufacture, cancer biology and epidemiology. In that way he provides the skeleton around which the flesh of the events of Toms River throughout the past few decades is built. He does this in a way that is accessible to anyone with a modicum of curiosity. No math needed! Yet the author doesn’t shy away from talking about the difficulties of epidemiology, modelling of water flow, and cell biology.

Some of what you read will shock you, some will enlighten, some will inspire. Five stars.


Christchurch Hospital’s latest study: IDENTAKIT-HF

If it weren’t for your kidney’s, where would you be? You’d be in the hospital or infirmary (with apologies to Fred Dagg). The heart and kidneys are not just linked by a pipe, but the health of one is very much dependent on the health of the other. Acute Kidney Injury (AKI) is a phenomenon whereby there is a sudden loss of all or some of the kidneys’ filtration ability. This can have dire immediate consequences with a greater increased risk of mortality & longer hospital stays. It can also increase the risk of developing a chronic kidney disease or even later cardiac problems. Unfortunately, AKI is devilishly difficult to detect, and therefore there are no early treatments. It is also very common – some 4-5% of all hospital patients. Those with heart failure are particularly vulnerable.

IDENTAKIT-HF is a new project all about identifying AKI biomarkers inheart failure. Two weeks ago it enrolled its first patient. It is a collaborative project involving myself, the Christchurch Heart Institute, and a biomarker laboratory in Prince of Wales Hospital, Sydney headed by former Christchurch nephrologist Professor Zoltan Endre. Not only are blood samples being taken from patients with heart failure and potential AKI, but also urine samples. This is because various novel protein markers in the urine appear to respond much more quickly to AKI than markers in the blood. It is now recognised, that not one marker, but a panel of markers is needed to identify AKI and provide information about how to target any treatments. IDENTAKIT-HF will identify the likely members of such a panel and then test if they really do identify the disease and predict its course. This will form the platform for future intervention trials to develop treatments and improve patient outcomes.

"Blausen 0246 ColorectalCancer" by Blausen Medical Communications, Inc. - Donated via OTRS, see ticket for details. Licensed under CC BY 3.0 via Commons - https://commons.wikimedia.org/wiki/File:Blausen_0246_ColorectalCancer.png#/media/File:Blausen_0246_ColorectalCancer.png

Blocked Bowel

The Press headlines this morning claim the Ministry of Health is blocking bowel screening tests. The article itself states the MoH does “not recommend” use of do-it-yourself bowel screening kits.  I can find no MoH press release relating to these kits, so I am a little confused as to whether or not the MoH is blocking anything at all.  This uncertainty aside, the issue has arisen because of the availability of bowel cancer testing kits which are self administered in the home and made available by the charity and advocacy group Bowel Cancer New Zealand/Beat Bowel Cancer Aotearoa (BBCA). There is evidently frustration within this group with respect to the government’s progress towards a bowel cancer screening program in New Zealand (there is currently a pilot underway).  My interest is not the politics, but merely to inform about the test.

The test being offered as best as I can make out is from Clinical Genomics and is their “ColVantage Home” test.  In the information on their website they give two numbers derived from trials which I believe are critical that any potential user of the test understand before they decide to use the test (indeed, not just for this test).  Those numbers are the sensitivity of the test, given as 86%, and the specificity given at 96-98%.  I expect to most those numbers are meaningless, and even to the scientist they are “minimal” in the sense no indication of how accurate these numbers are given (think “margin of errors” given in political polls).  However, let me take the numbers as gospel and let you know what they mean.

The False Positive.  I'd love to acknowledge the source, but I can't locate them.

The False Negative. I’d love to acknowledge the source, but I can’t locate it.

First, a sensitivity of 86%.  This simply means that for every 100 people who actually have bowel cancer, 86 will test positive with the home kit.  The very very important fact to note here is that a negative test does not mean you definitely do not have bowel cancer.  The 14 missed cases are called False Negatives, or Type II errors and are beautifully illustrated by this classic infographic of the doctor failing to diagnose pregnancy.  My concern with False Negatives and a “home kit” is that some people may feel falsely reassured with a negative test.  On the other hand, a test administered by a medical doctor is not simply the test, but exposure to the doctor who may see other signs or symptoms that the test doesn’t pick up.




False positive

False positive

On the other hand a 96-98% specificity means that for every 100 people who do not have bowel cancer 2 to 4 will test positive.  That is, a positive test does not mean you definitely have bowel cancer. The missed 2 to 4 cases are called False Positives, or Type I errors as illustrated by the diagnosis of the man in the image.

Another way of thinking about this is that all of us before a test have a certain probability of having bowel cancer.  We may get an idea of what that probability is by knowing the rates of bowel cancer amongst people like us.  In New Zealand the rates are very high – some of the highest in the world at about 0.3% or 300 per 100,000 adults.  However, risk is higher as people age, hence screening programs are targeted at older adults (over 50s in this case).  There are other risk factors.  Check out the risk calculator here.  A positive test essentially increases your risk, but not to 100%, and a negative test, decreases it, but not to 0%.  If it was me, and I was worried enough to want to have a test because of increased risk factors, I’d go and ask my GP for one.  On the other hand, if I didn’t want my wife to know (duh!) and got a kit, and it was positive, I’d also head down to the GP.

As I stated before – beware of being falsely reassured by a negative test.  However, there is also a major issue with false positives which bedevil any screening program, and even more so one in which the most at risk population are not being targeted (in this case there is nothing stopping 30 year olds having tests).  This requires a bit of maths.  Let’s pretend for a minute that the tests are only being done by people in a population with a very high prevalence of bowel cancer – say 1%.  That means that for every 10,000 people tested 100 will have bowel cancer for whom 86 the test will be positive.   Of the 9,900 who do not have bowel cancer, 198 to 396 will also test positive – ie falsely positive.  ie, in total, 284 to 480 people will test positive.  ie 22% to 30% of those who test positive actually have bowel cancer.  For the individual who started knowing they had (say) a 1% risk, they now know they have a 22 to 30% risk.  Certainly worth checking out more.

Of course, if people have these tests regularly, the proportion of people who end up having a false positive test at some time will increase (along with the proportion of people with bowel cancer who have a positive test).  ie repeat testing will increase sensitivity and decrease specificity.

Finally, if you have a history of bowel cancer in your family then don’t hesitate to ask your GP for tests and advice on what you can do to minimise your risk through improving your life style.


Two minds about funding heart research

Recently I had a knock on the door from an enthusiastic young man talking about heart research. Given that has been the focus of my research for the last 18 months or so I was delighted that someone was out there trying to raise money for research. However, my delight was, in retrospect,was tempered somewhat when I realised that the man was not representing a New Zealand based research group.

The man was collecting donations for the Heart Research Institute, an independent research group based in Sydney Australia. This is a substantial and credible organisation. I would be happy to collaborate with any of their team leaders. Looking at their website I noted one (of 12) research groups mentioned New Zealand collaborators.   I’ve written to ask if they have more. The HRI have a very professional New Zealand website which gives information on heart disease statistics in New Zealand. They indicate that they support scholarships and fellowships for New Zealanders to work with their Australian counterparts. However, I am in two minds about this group door knocking in New Zealand – one mind thinks “great” they are keen to raise money for heart research, what a good cause. The other thinks “hmmm,” don’t we have some wonderful New Zealand based heart research groups and charities – why another (not New Zealand based) one in a crowded field seeking money from a limited pool of discretionary spending?

Perhaps, to help the people of Canterbury and wherever else funds are being solicited from to make up their own minds, I can remind people of four great charitable organisations supporting heart research in New Zealand.

Heart Foundation of New Zealand: This is a wonderful organisation with a long history of supporting research in New Zealand as well as supporting individuals within New Zealand. They are the group behind the “Heart Foundation Tick” on food labels. Their website is really worth checking out… I just learnt about the “Two Ticks” now appearing on some labels. For the likes of a researcher like me they provide small, but very important, grants that enable important questions to be answered. Indeed, I have just had a paper published which a Heart Foundation grant made possible. In that paper we show that one of the latest guidelines on how to use a blood marker (used in most New Zealand hospitals) to rule out someone having a heart attack are flawed. I note, that they have in large letters on their web site that they do not do door to door fund raising.

Christchurch Heart Institute: CHI is a research group and charitable organisation within my own department, the Department of Medicine, at the University of Otago Christchurch campus (known to most Cantabs as “the med school”). Headed by Professor Mark Richards it is a world renowned group. I have the privilege (a little daunting given just how incredibly intelligent these people are) to collaborate with CHI on a number of clinical projects. The publication I mentioned was one of them. Another project, just kicking off, is investigating markers of acute kidney injury within people who have acute heart failure. They have recently expanded into social media – so you can follow them on facebook.

Canterbury Medical Research Foundation:  CMRF is a wonderful organisation – they are one of the three major sponsors of my own fellowship. My own prejudice aside, CMRF have been supporting research in Canterbury for over 50 years. One aspect of the CMRF that really impresses me is that they understand the need to support researchers and just “let them get on with it.” Cantabrians may recognise their recent campaign that has included some impressive billboards. One important plank of CMRFs work in Canterbury is their subsidiary the New Zealand Brain Institute which does important research into stroke, Alzheimer’s and Parkinson’s disease.

Emergency Care Foundation: The ECF supports research in the Emergency Department of Christchurch hospital including research into the rapid rule-out of heart attacks for patients presenting with chest pain.  I’m fortunate enough to be involved in that research and the role out of new diagnostic pathways to all emergency department in the country.  ECF also support research into the health affects of the Christchurch earthquakes.  ECF are another of my major sponsors.

Some logos of the great local charitable organisations supporting heart research