Are We at a Tipping Point for Open Data?

18 Mar

Ha-Vinh:

Data sharing is on the rise, the French public health insurance shares openly its data as you can see in the link below:
https://www.etalab.gouv.fr/ouverture-du-fichier-damir-par-lassurance-maladie

Originally posted on The Scholarly Kitchen:

Street sign, park nearby Image via RP Norris https://www.flickr.com/photos/rptnorris/3453936781/

Last month, President Obama showed off his dad-joke skills while announcing the appointment of the first US Chief Data Scientist. The focus of much of the White House’s messaging around this appointment has been on making the government’s own data publicly available. In his ‘memo to the American people’, however, Dr. D.J. Patil talked about acting as a conduit between government, academia and industry. In some ways, this latest move can be seen as a continuation of a US government push toward open data that mirrors efforts in Europe and elsewhere.

For a long time, there has been an expectation that researchers share data upon request with other academics but more recently, the trend has been towards making data widely and publicly available. In February 2013, the White House Office of Science and Technology Policy released a memorandum on Expanding Public Access…

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In Support of Academic Writing

27 Feb

Originally posted on Explorations of Style:

Last fall, Steven Pinker promoted his new book, The Sense of Style, with an article in The Chronicle Review entitled “Why Academics Stink at Writing”. I didn’t write about this article at the time because I hadn’t yet read the book; while I had a lot of concerns about the article, I was reluctant to share them in the absence of an understanding of his overall intentions in the book. Over the winter break, I read the book in order to write a review; what I found was a thoughtful diagnosis of the habits that impede strong academic writing and a great deal of incisive writing advice. I recommend Pinker’s account of how what he calls the “curse of knowledge” (p. 59) prevents us from grasping what the reader needs to know. And I recommend his approach to managing complex writing, especially at the sentence level. I feel certain that most serious…

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What a good introduction paragraph looks like?

8 Feb

Putting their research in context is of a major concern for all the health services researchers. This comes from the fact that health services research is not per se a hard science. Its research object is transversal over a large range of domains extending from occupational medicine to surgery passing by pharmacology and social sciences. Thus the importance of a strong introduction in our papers, expliciting what our research confirms or questions in the existing knowledge and what new knowledge it adds. There is no question to be able to do that without conducting beforehand a sound analysis of the literature. H Maisonneuve in his blog gave an interesting link to the Lancet’s definition of what a good introduction should look like in a medical research paper:

This Is What a Strong Introduction paragraph Looks Like:

introduction

 

writing a journal article? start with the So What question

6 Jan

Originally posted on patter:

I’m running another writing course soon in Iceland and have been sorting through potential pre-reading material. In my file of pdfs I came across an editorial written by Neil Selwyn in the journal Learning, Media and Technology. The piece is called ‘So What?’… a question every journal article needs to answer‘.

It’s pretty apparent that Selwyn was tired of getting papers that weren’t suitable for his journal. In his three years as Editor he’d obviously seen a lot of unsuitable submissions – and he really, really didn’t want to see any more. You can hear his frustration in his very clear delineation of what is and isn’t acceptable for his journal….

These ‘proof of concept’ and ‘best practice’ studies of the application of specific digital devices and practices in particular educational settings are clearly necessary and worthwhile stages in the development of any educational technology. Yet work of…

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Multiple sclerosis, what about the south-north gradient?

4 Jan

Recent researches found that the south north gradient of the occurrence of multiple sclerosis is diminishing in the USA and doesn’t exist anymore in France.
Here are the two articles:

Alvaro Alonso, MD Miguel A. Herna ́n, MD
Temporal trends in the incidence of multiple sclerosis A systematic review
Neurology 71 July 8, 2008
Available in full text here:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109189/pdf/129.pdf

Fromont A, Binquet C, Sauleau EA, Fournel I, Bellisario A, Adnet J, et al. Geographic variations of multiple sclerosis in France. Brain 2010;133:1889-99.OpenUrlAbstract/FREE Full Text http://brain.oxfordjournals.org/content/brain/133/7/1889.full.pdf

Thus the epidemiology of multiple sclerosis seems to shift toward a less intense south north gradient but in the same time an aggravation of the sex ratio, aggravating the burden that women bear in this inflammatory disease that affects the central nervous system (i.e. the central unit of our body in terms of information technologies).

This tendency opens new interests for more epidemiological studies in this field. All the more because the observational studies aiming to prove the mixed, genetic and environmental, etiology are entangled with the current migrations of populations, the mobility of young people in view of finding a job and the changes in life habits in the populations of the south such as using more protection against the sun rays.

Professor Confavreux had well depicted the stakes in this editorial:

An unchanging man faced with changing times Christian Confavreux
DOI: http://dx.doi.org/10.1093/brain/aws135 1663-1665 First published online: 24 May 2012
http://brain.oxfordjournals.org/content/135/6/1663.full

For the present moment multiple sclerosis etiological mechanism is an enigma and risks to remain so if researchers in the domain have no new data to crunch at the populational level.

The Craft of Revision

19 Dec

Originally posted on Explorations of Style:

All academic writers have some sort of revision process, but that process is often either insufficient (just nibbling around the edges) or scattershot (catching some things but missing others). To improve our revision practices, we generally have to both deepen them and make them more systematic.

My starting point here is the near impossibility of crafting reader-ready first drafts. If the material is conceptually complex, if you are still struggling to understand the implications of what you’ve learned, if the internal connections aren’t yet apparent to you, then the first draft is going to be clumsy. At that stage, the text will be something that you are still learning from rather than something that others can learn from. For most of us, making the transition from a text that helps you to a text that helps the reader takes multiple iterations. When I talk about needing to make a commitment to extensive revision, that choice of words…

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The value of identifiable research data

16 Dec

Joel Kallich of Big Health Data wrote me: Over the last 30 years, the government has been reluctant to release identifiable information, first on an

via The value of identifiable research data.

The neuroscience of meditation

16 Dec

Life is a permanent flow: one has to let go the past and present in order to authorize freely the next event of one’s life to happen. If not, a damp will interrupt the flow, which is not a good thing from a sound and balanced living perspective.

One has to live a life which is intrinsically ever changing, and thus which is anxiety provoking.

The only thing that is permanent is one’s awareness of being present in the present moment, which by itself is a blessing one should be grateful for .
At that point meditation, wether by focusing on an action like breathing or walking or by observing with detachment the course of our thoughts and feelings created by our mind or by exercising compassion and loving kindness towards other sentient beings can be of some help.

By the way it has been demonstrated by neuro-scientists that meditation modifies the way the brain functions and even the size of some brain regions.

I read an article on this subject in the November 2014 edition of the journal Scientific American entitled Mind of the Meditator, authored by Mathieux Ricard a Buddhist Monk, Antoine Lutz a research scientist at the Frenh National Institute of Health and Medical Research and Richard J Davidson from the University of Wisconsin-Madison.

They conclude that
even with the requisite cautions, research on meditation provides new insights into methods of mental training that have the potential to enhance human health and well-being”

Violence and categories

29 Nov
We should not anymore talk about, or show violence in terms of, (or focusing on) the category that the perpetrator of the offense belongs to (eg male vs woman, Jew vs Palestinian, terrorist vs citizen, human vs animal and so on). Because it only aggravates the hate and further divides humankind or sentient beings. Instead of being reduced to categories violence must be shown only as a sin or an offense and a crime each individual should refrain to commit even under certain attenuating circumstances (bad education, unhappy childhood, fear, anger, prior offense …) and everybody should be warned against committing it no mater the category one belongs to (see categories above: female or male and so on..). This kind of perspective aggravates in my view and enlarges the gap between individuals by tacitly defining the perpetrator as a “category” broadly speaking. Hurting someone has nothing to do with the category one belongs to, it is above such a consideration and is an absolute interdict (the bible cites only the neighbor as the unique category encompassing all other categories). If not categories could be used as an excuse or at least an explanation in the mind for the perpetrators. Our modern societies should go one step beyond by denouncing violence against fellow human at large or, even more, against sentient beings at large, without doing anymore any categories in the discourse by doing that.

 

Time series: what conclusions can we draw from ?

8 Nov

Here below is a link toward a time series published by the French Agency for pharmaceutical safety (aka ANSM). Although the method is well described and doesn’t raise any concern, nevertheless the interpretation that is done from the results in the discussion is subjected to caution.

My expression of concern is motivated by the fact that the authors of the study link the lowering of the incidence of pulmonary embolism to the lowering of sales of third and fourth generations of contraceptive pills.

Indeed a cofactor can explain the concomitant lowering of both time series:
the large warning campaign in the medias with messages about a) the risks attached to those third and fourth generations of contraceptive pills AND b) the risks of pulmonary embolism (ie blood clots in the lung) every woman faces under contraceptive pills, no matter the generation of the contraceptive pill.

Thus the practitioners could have been more attentive to the risk for all their patients and stopped the contraceptive pill, even for the first and second generation of pill, in case of any doubt (eg a phlebitis of the leg or a tobacco addiction).

One thing is for sure: the results of this study show that the campaign in the media had an impact in term of public health, but no causality can be formally drawn between the lowering of the sales of the third and fourth generations of contraceptive pills and the lowering of pulmonary embolism from the results of this study.

The study:

Etude de l’impact de la modification récente des méthodes de contraception sur la survenue d’embolies pulmonaires chez les femmes de 15 à 49 ans (07/11/2014) application/pdf (316 ko)

http://ansm.sante.fr/content/download/69461/886199/version/1/file/Etude-COC-Embolie-pulmonaire2014.pdf

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