A real life Periodic Table is a post from: Sciencebase Science Blog

Yes, I’m back from participating in the Fenland Study. It’s the full body M.O.T. test courtesy of the Medical Research Council (MRC) Epidemiology Unit.

The urine and bloods will be tested for various disorders, kidney function, liver disease and most importantly for this study, perhaps, diabetes (hence the glucose drink).

DEXA’s midday stunner

The X-rays amount to an additional half hour of background radiation exposure (unlike a conventional chest X-ray, for instance, which is about five-days worth). That scan – dual-emission X-ray absorptiometry (now known as DXA, previously DEXA) is used to determine bone mineral density (BMD) and body fat distribution. The process involves lying on a bed, keeping very still and having two X-ray beams of different frequency, or energy level, aimed at your body. The scan is akin to scanning a document on a flat-bed scanner. Anyway, the picture you see here, is how I look underneath my tee-shirt and scrubs and, in fact, underneath my skin! DXA is the most widely used and most thoroughly studied BMD measurement technology. If you’re at risk of osteoporosis they’re likely to use this scan to assess you.

Anyway, the Fenland Study has been underway since 2005 and randomly selects from patient registers for the regions surrounding Cambridge, Ely and Wisbech. The team recently passed the 5000th person born between 1950 and 1975 and is hoping to assess 5000 more, which will give the research team an excellent over-view of fitness, body metrics and metabolic issues across the population. Interestingly, they recruit people without diabetes and according to a wallchart published at the time they’d assessed 2387 people, they’d spotted 31 undiagnosed cases of type 2 diabetes.

I’ll receive a report some time after I send back the heart monitor and GPS tracker, this will include details of what they found and presumably any suggestions regarding lifestyle, diet and exercises that might be warranted. My physician will also receive a copy of the blood test results and will hopefully not have to give me a follow-up call.

The research at the MRC Epidemiology Unit, which is running the Fenland Study focuses on several key areas:

• The causes of type 2 diabetes and obesity
• The effect of diet and nutrition on type 2 diabetes and obesity
• The effect of physical activity on type 2 diabetes and obesity
• Early growth and development in children and how this affects the likelihood of developing type 2 diabetes
• Strategies for preventing type 2 diabetes, obesity and their related complications

If you get to take part you will not only be assisting medical science and a worthwhile cause you will be saving yourself a few pounds as the whole battery of tests would normally cost about 600GBP to undertake at a UK hospital. All members of the research team are highly skilled, very professional, courteous and offer you a cuppa and a sarnie when they’re finished with your body. Who could ask for anything more?

You cannot ask your GP or anyone else for that matter to add you to the study list, it’s done randomly, but if they offer you the chance to take part, grab it.

Feeling fine for Fenland findings is a post from: Sciencebase Science Blog

Indeed, it was only a clutch of non-Einsteinian pseudoscientists with their cracked conjectures who even vaguely thought such particles might achieve such great speeds. After all, there is no way to explain how a particle with mass might be accelerated to a speed that exceeds that of “mass-free” electromagnetic radiation, this is regardless of any discrepancies in Relativity or the fact that it is yet to be unified or corroborated with the quantum world. More to the point, the very GPS satellites on which many scientific studies rely have to be corrected for Relativistic effects, which kind of suggests that it’s a pretty accurate interpretation of physical reality!

Anyway, just released a CERN Communiqué de Presse which says:

“The OPERA collaboration has…identified two possible effects that could have an influence on its neutrino timing measurement. These both require further tests with a short pulsed beam. If confirmed, one would increase the size of the measured effect, the other would diminish it.”

I suspect that the OPERA team will not be offering to pass the condiments to Jim any time in the near future.

“The first possible effect concerns an oscillator used to provide the time stamps for GPS synchronizations. It could have led to an overestimate of the neutrino’s time of flight. The second concerns the optical fibre connector that brings the external GPS signal to the OPERA master clock, which may not have been functioning correctly when the measurements were taken. If this is the case, it could have led to an underestimate of the time of flight of the neutrinos.”

The new measurements with short pulsed beams are scheduled for May, CERN says.

Faster than light? Jim’s shorts are safe is a post from: Sciencebase Science Blog

If you have an iPad or use another iOS devices (iPod Touch, iPhone) you can view Sciencebase (with tech news incorporated from sibling site Sciencetext.com and chemistry news from ChemSpy.com in the all in one “Sciencebase app“. You can also still add the Sciencebase webfeed (newsfeed, RSS, call it what you will) to your Google Reader, Feedly, Zite, or FlipBoard and see headlines and full-text as soon as new posts appear here.

There is also now the Sciencebase Twylah page, which automatically determines the most active Twitter topics and posts and gives you a magazine-like display of my offerings on the microblogging site.

Thumbnails for Sciencebase and connected sites and places you will see the David Bradley byline are collected on the Sciencebase Tizmo page.

Filling up on Sciencebase is a post from: Sciencebase Science Blog

It’s uncomfortable but avoids the need for anaesthetic drops in the eyes and means your eyes are not being impinged by a plastic or metal disc as with the old sprung devices.

My ophthalmologist knew the principles of intraocular pressure and why she was measuring it, but wasn’t so sure how the device actually “read” the pressure. Like I say the device simply times the gap between puffing the air and the distortion of the cornea as the air hits, which is calibrated with eye pressure. It’s a process that occurs on a timescale of thousandths of a second, milliseconds. Critically, it takes less time for the puff of air to flatten a soft eye than it does a hard eye. A harder eye is one with a higher intraocular pressure and thus a greater risk of glaucoma.

My pressures were fine, although a slight discrepancy between eyes meant the ophthalmologist wanted to carry out a follow-up test. To be honest, from this site, I’d have been inclined to ignore the outlier she saw with my left eye and to assume the difference was down to her testing the right eye first. As I said, it’s an uncomfortable feeling having air puffed repeatedly in your eye and it does make you tense and squint.

Anyway, the follow-up test is a vision field test, which involves staring at a marker on a screen in a darkened room and indicating when and how many dim spots of light appear as generated by a computer. Thankfully, my field test was fine. Oddly though, my ophthalmologist took several attempts to get defeat my vision, raising the point that maybe I could see in the infrared. It’s not that, I just eat a lot of carrots.

More on non-contact tonometry here.

Glaucoma is an eye disease in which the optic nerve becomes damaged because of increased fluid pressure in the eye. The term ‘ocular hypertension’ is used for people with consistently raised intraocular pressure without any associated optic nerve damage. Conversely, the term ‘normal tension’ or ‘low tension’ glaucoma is used for those with optic nerve damage and associated visual field loss but normal or low pressure.

Detecting glaucoma is a post from: Sciencebase Science Blog

Thanks to Jen Gristock for alerting me to this marvellous news. Other guest stars in the new series will include Rupert Graves, well known as Detective Inspector Lestrade in Steven Moffat’s other show Sherlock (Dr Who is basically Sherlock with a sonic screwdriver, Tardis and alien nasties, and Prof Moriarty simply becomes The Master). Mark Williams (of Fast Show fame who also plays alongside Bradley in the Harry Potter movies as Arthur Weasley and was recently a vampire historian in Being Human).

Intriguingly, the original Paget illustration of Moriarty bears an uncanny resemblance to that David Bradley…and if he wore reading glasses, probably to me too…

David Bradley to guest star in Dr Who is a post from: Sciencebase Science Blog

Interestingly, electromagnetic radiation features in the news today as politicians are once again concerned about the devastating effects a pulse of electromagnetic radiation either from the sun or from a nuclear weapon detonated high above a country.

Google Love Hertz is a post from: Sciencebase Science Blog

There are numerous ways to apply statistical analysis each with its own merits and limitations. Two of the most fundamental are:

• Regression
• Time series analysis

Khalil Al Jerjawi of the University of Western Sydney, discusses the application of these statistical tools in management research in a forthcoming issue of IJLSE.

Regression

“Regressions are used to compare the effects of two or more independent variables on a dependent variable,” he explains. There are numerous regression techniques including linear regression a parametric technique in which the regression function is defined in terms of a finite number of unknown parameters based on experience with the data). However, there also are non-parametric regression techniques that can be multiply dimensional.

Regression analysis can be used to extrapolate data, a point often exploited in making wild predictions and forecasts based on the perception that a trend will continue even if data is limited. However, application of regression relies on assumptions about the data and can lead to spurious results if data sets are relatively small or there are many outliers in a sample. Aside from wild extrapolations, regression often leads to the conclusion that because two or more variable are correlated that the correlation means one causes the other, this is not necessarily the case. The number of calls to the emergency fire services rises as the number of fires increases, this does not imply that calls to the emergency services cause fires.

Time series analysis

A time series is nothing more than data collected at uniform time intervals. The daily closing prices of Dow Jones index or the height of the Nile River at Aswan, for example. Time series analysis then uses various techniques to pull out the characteristics of the data from the series and, of course, to use this to predict the next data point in the series. Depending on the data being sampled this can be straightforward and reliable, perhaps as with rivers, or entirely spurious as is more common with finance. Time series analysis of climate data are the perfect example of how statistics can be manipulated to prove or deny a “fact”.

Obviously, by definition, time series are ordered. This is in stark contrast to other data sampling techniques. For instance, it doesn’t really matter in what order you count the fruit hanging on apple trees in an orchard to assess fertiliser quality, but it does matter if you’re monitoring the impact of daily temperatures rises and falls on when the fruit ripens. Similarly, time series analysis is distinct from spatial data analysis where data points are recorded in relation to geography (where the trees are in relation to the farm buildings and walls, for instance. According to Wikipedia: “A time series model will generally reflect the fact that observations close together in time will be more closely related than observations further apart. In addition, time series models will often make use of the natural one-way ordering of time so that values for a given period will be expressed as deriving in some way from past values, rather than from future values.” The trap that those interpretating time series can fall into is that past events are not necessarily a good predictor of future outcomes in many, many cases.

We all know of countless studies that seemingly contradict each other. The climate change “debate” is perhaps one of the most controversial, although the case for vaccination, for genetically modified food, for pharmaceutical intervention in medicine all succumb to the intrinsic assumptions of statistics and the willingness of the media to manipulate them to their own ends. One week, coffee causes cancer, the next the antioxidants in coffee prevent cancer. Yesterday, red wine was anathema, tomorrow it’s the best thing since…it’s not as if it’s the same data sets being interpreted.

Khalil Al Jerjawi (2012). Methods of statistical analysis: an overview and critique of common practices in research studies Int. J. Liability and Scientific Enquiry, 5 (1), 32-36

Lies, damned lies and statistics is a post from: Sciencebase Science Blog

Multivariate statistical data processing has been used to create a model from gas chromatography-mass spectrometry (GC-MS) data of metabolite profiles of the various types of Mycobacterium species tuberculosis (TB). The model could allow diagnosticians and biomedical researchers to quickly and easily distinguish between various infectious Mycobacterium species – TB news.

When graphene is stimulated optically it produces a photocurrent on a time scale of mere picoseconds. A German research team has now used the pump-probe method of time-resolved laser spectroscopy to take a snapshot of this process as it happens – Atomic Absorption and Atomic Spectroscopy Resource.

Nuclear magnetic resonance spectroscopy, mass spectrometry and other techniques have been used to demonstrate that the consumption of toxic mushrooms may have been responsible for a series of unexplained deaths in China during the last three decades – NMR and toxic toadstools.

X-ray computed tomography can be used to look closely at superhydrophobic polymer meshes. These experimental materials have been shown to trap drug molecules with a barrier of air between them and an external aqueous environment – Drug smugglers.

Science, spectroscopy and stuff is a post from: Sciencebase Science Blog

There are obstacles to full-scale adoption, not least the fact that 300 years of tradition are not quietly overturned despite the desires of those who have laid bare the flaws. While many scientists recognise the benefits, there are concerns that these new forms of publication and education can take a lot more time and effort and at a time when economic strife is a seriously limiting factor (as it always was), the inclination to overturn the system may be there but the power…the money…to do so may be absent. Then there are the concerns regarding whether one’s output might be used without citation.

Again, it’s an old issue, couched in modern terms. Creative Commons licensing exists and some are willing to share their rights and go copy left with or without attribution or credit, others are not. Perhaps one of the most important issues that has been with us throughout human history is that one may expend energy and reap none of the rewards. Indeed, competitors may gain advantage from one’s efforts. Many of us are all for altruism, but generally not if it leads to our own personal demise.

Peter Kraker and Günter Beham of Graz University of Technology, Austria, Derick Leony of Carlos III University of Madrid, Spain and Wolfgang Reinhardt of the University of Paderborn, Germany, writing in the IJTEL make the case for open science in technology enhanced learning. In their view, “Open science means opening up the research process by making all of its outcomes, and the way in which these outcomes were achieved, publicly available on the World Wide Web.” I assume they actually mean the wider Internet, given that many of the tools available may not necessarily be part of the Web, but you get the idea. They suggests that adopting open science could bring together disparate communities as well as leading to open methodology so that researchers in the field can work with the materials and tools made available and reproduce (or not, as the case may be) research results.

Of course, concepts are one thing. The best laid plans of mice and men, and all that. But, what is now needed for open science to progress are evangelists, people to spread the good word and to share the benefits and actually the disadvantages too. To bring the community together and to find a way forward, not only in TEL and TEL research but in the wider realm of science. “It is crucial to make the research community aware…and to support researchers in use and re-use of the available data and other [resources],” the team concludes.

Peter Kraker, Derick Leony, Wolfgang Reinhardt, & Günter Beham (2012). The case for an open science in technology enhanced learning Int. J. Technology Enhanced Learning, 3 (6), 643-654

Related articles

• The difficulties in opening science: Q&A with Michael Nielsen (ted.com)
• Open science: why is it so hard? (downes.ca)
• Testify: The Open-Science Movement Catches Fire (biosingularity.com)
• Advocates For Open Science Say Systemic Change Is Inevitable (keptup.typepad.com)
• Open access science (energybulletin.net)
• ‘Open Science’ Challenges Journal Tradition With Web Collaboration – Thomas Lin via NYTimes.com (stoweboyd.com)

Open science – just do it is a post from: Sciencebase Science Blog