Health on Jean-Etienne's blog

COVID-19 cases in Maryland congregate living facilities

Sun, 15 Nov 2020 14:31:07 +0000

Five months ago, I was wondering why Maryland remove COVID-19 cases from its count in congregate living facilities (nursing homes, prisons, …). I still don’t have any answer but I found a technical solution :-)

The Python script (in src/ in the MD-coronavirus repo on Github) just fills in the latest data for days where data is missing. On a side note, it also fix some basic issues like a reporting date in year “0200” (instead of “2020”). You can play with the fixed data file here.

COVID-19 cases in Wallonia schools

Mon, 26 Oct 2020 23:25:29 +0000

In Wallonia (Southern part of Belgium), universities are already back to only giving online classes, schools will be closed two additional days after the Autumn holidays (so November 2-11), and secondary schools (12-18 years-old children) will be virtual for the 3 days before the Autumn holidays (so October 28-30). The reason? The exploding number of COVID-19 cases in schools.

In Wallonia, education is in the hands of the French-speaking Community (along with Brussels) but its statistics department doesn’t seem to provide public data on COVID-19. For that, we have to look at ONE (roughly: " Office for births and infancy") that communicate weekly numbers of cases and quarantines in children in schools via press releases (forcing us to parse PDFs but it’s better than no data).

COVID-19 clusters in Belgium

Mon, 19 Oct 2020 22:15:08 +0000

Recently (I’m writing this on October 20), the (new) Belgian government decided to apply more stringent prophylaxis measures to contain COVID-19. One of the controversial measure is to close bars and restaurants for a month.

Unfortunately, in a way, at approximately the same time, AVIQ released its latest poll on COVID-19 clusters in Wallonia ( AVIQ is the Walloon agency for well-being, health, handicap and family). I wrote it was unfortunate because I read and heard several people who criticized the closing of bars and restaurants by citing this poll. But this poll cannot answer in favor or against this closure; it doesn’t look at that …

A third of Maryland counties tested more than 25% of residents

Tue, 11 Aug 2020 15:25:11 +0000

Sometimes, you think that you found something interesting but the Maryland Department of Health is already presenting it on its COVID-19 dashboard :-D

For instance, I calculated the percentage of residents of the different counties ever tested (regardless of the test result). I found out that a third of Maryland counties (8/24) tested at least once more than 25% of their residents. Indeed, as of yesterday (August 10), here are the counties in that category:

COVID-19 hospitalization by age in Maryland

Sun, 09 Aug 2020 17:37:08 +0000

Since mid-July 2020 in Maryland, we understood that the 20-59 yr age group was problematic, especially the 20-29 yr age group that is racing to overtake all age groups in terms of number of COVID-19 cases (relative to their population, see top chart below).

In terms of COVID-19 hospitalizations, we also saw a small rebound (see chart below; it seems that it subsides since beginning of August).

But what we didn’t know (for this small peak as well as since the beginning) was what is the age of these hospitalized populations. Did these hospitalizations impacted more the older adults? The younger ones? Or the children? The Maryland Department of Health COVID-19 dashboard doesn’t report that information (nor in the API).

Moving from US to Belgium during a pandemic

Thu, 06 Aug 2020 19:13:34 +0000

We moved our family from the US (Maryland, just in case you didn’t know yet) to Belgium - no big deal. During the COVID-19 pandemic, in July-August 2020 - now we’re talking …

I wrote this post to document our journey. We were (and still are) extremely privileged to have been able to do this, in the conditions we did it. The journey is not over. I’ll update and continue to document it until we fall back into something more “normal” … [long post]

What does release from home isolation mean in Maryland?

Wed, 05 Aug 2020 11:05:10 +0000

Since the beginning of this pandemic, one metric intrigued many of us in Maryland: the cumulative number of people released from isolation. Initially (before the data release via API, when there was only the MDH dashboard), it was even thought to be the number of hospital patients released from isolation. It’s not: the API page mentions:

Total Number Released from Isolation data layer is a collection of the statewide cumulative total of individuals who tested positive for COVID-19 that have been reported each day by each local health department via the ESSENCE system as having been released from home isolation. As “recovery” can mean different things as people experience COVID-19 disease to varying degrees of severity, MDH reports on individuals released from isolation. “Released from isolation” refers to those who have met criteria and are well enough to be released from home isolation. Some of these individuals may have been hospitalized at some point.

A first insight on COVID-19 contact tracing in Maryland

Mon, 03 Aug 2020 21:47:09 +0000

I may have missed when the data was first released but I discovered the Maryland Department of Health (MDH) is publishing some data about COVID-19 contact tracing (in Maryland). This data is not on the main COVID-19 dashboard but on the contact tracing page (and in the datasets that can be downloaded). Here is a first insight of what happened so far …

Note: if you just look for where to get tested in Maryland, the official information is here.

What is the COVID-19 positivity rate in Maryland?

Mon, 27 Jul 2020 03:32:50 +0000

Every day, Governor Hogan and members of his team are communicating news on the COVID-19 situation in Maryland via Twitter (and other media): @GovLarryHogan, @riccimike, @katadhall, … (and of course: @MDHealthDept too!). A number of data enthusiasts are also parsing the MD Department of Health data: @TylerFogarty7, @MikeBReporter, @JauquetW, @PrayagGordy, … and of course: @jepoirrier) … And this is only on Twitter!

But also every day, there is one thing that constantly changes: how everyone is calculating the COVID-19 positivity rate. Today (July 26), for instance, the different daily positivity rates announced are: 3.77% ( Hogan), 4.47% ( Hogan again in the same tweet, Hall, Ricci, MD Health Department, Fogarty) and ~6% (for me, the exact number behind the ~ is 6.14%). This doesn’t show the 7-days (or n-days) averages and other measures. And this is only on Twitter.

Gender of COVID-19 cases and deaths in Maryland

Wed, 15 Jul 2020 02:37:12 +0000

After my previous posts about age of COVID-19 cases and deaths in Maryland, it was logical that I write about the gender of these cases and deaths. Rest assured: this time, it will be much shorter ;-)

Indeed, in a nutshell, in Maryland (like in the rest of the world), women are more impacted than men by the disease. But men are dying of the disease a little bit more than women.

Note: this post was updated on July 15, 2020, to fix an error in my code!

Age of COVID-19 deaths in Maryland

Fri, 10 Jul 2020 03:51:31 +0000

After my previous post on the age of COVID-19 cases in Maryland, it was logical that I write about the age of COVID-19 deaths in Maryland. So far, media and State Departments of Health all agreed that the older someone is, the more risk this person has to die from coronavirus.

So far, this is unfortunately also true in Maryland. In the graph below, we clearly see that people 50-59 years old have more than 250 deaths, people 60-69 have more than 500 deaths, people 70-79 have more than 750 deaths and people 80+ have nearly … 1,5000 deaths! The graph at the bottom also clearly shows that people in age categories 60 and above provide most of the new daily deaths due to COVID-19 (even if we came back down from a peak at about 40 deaths in 80+ at the end of April).

Age of COVID-19 cases in Maryland

Thu, 09 Jul 2020 13:02:00 +0000

We recently heard in the US media that, if COVID-19 affected more the older population, beginning of 2020, the younger population was now more affected, especially young adults (various reasons were mentioned: the various academic breaks, being more active or “forced” to work, the sentiment of invincibility …). I wanted to see if one could see a similar trend in Maryland.

If you look at the section of the Maryland population by age (graph below), as of today (July 9, 2020), you see that cumulatively, people 30-39 have the majority of cases, followed by people aged 40-49, 50-59 and 20-29 years old. There are relatively few cases above 70 years old and fewer cases below 20 years old.

Why would Maryland remove COVID-19 data from nursing homes?

Fri, 26 Jun 2020 03:16:33 +0000

Since the beginning of the COVID-19 pandemic, we suspected and saw that nursing homes and other facilities where people are grouped together (prisons, …) could be at higher risk of transmission. The focus on nursing homes was because deaths seem to disproportionately affect the older population that also resides there. And nursing homes are also home for frail people with comorbidities.

In its dashboard, the Maryland Department of Health quickly started to build a dedicated page with numbers from different “congregate facility settings”. As I did for other metrics from this dashboard, I made a chart of what seemed the cumulative total cases, differentiating staff (who are stuck working there) and residents (who stuck living in these facilities):

COVID-19 inequalities in Maryland

Sat, 13 Jun 2020 01:54:42 +0000

The recent Black Live Matters protests made me think a lot - as a white man, as a husband and dad, as a biologist by training, as a health economist by day, as someone interested in COVID-19 data where I live by night … as a human, in summary. I don’t have grandiose pieces of advice or any deep thoughts, not for here (but if you call me, we can talk ;-)). Here, let’s continue our exploration of COVID-19 data in Maryland.

Weekly seasonality in COVID-19 deaths reported in Maryland

Wed, 03 Jun 2020 21:58:48 +0000

On its dashboard, the Maryland Department of Health is reporting confirmed deaths due to COVID-19 in two ways: by date of report and by date of death (updated as amendments to the death record are received). The definition of confirmed death is:

A death is classified as confirmed if the person had a laboratory-confirmed positive COVID-19 test result.

What I was intrigued is that reporting seems to follow a pattern influenced by the day of the week (see figure below). The top chart (cumulative) is just an addition. A plateau would be welcome: it would indicate death rate is slowing down. Today, the COVID-19 death rate is 41 / 100,000 population. The bottom chart shows the number of deaths due to COVID-19 reported each day: the black line represents the number of deaths each day they were reported; the grey line represents the number of deaths each day they occurred.

A glimpse at COVID-19 cases in some Maryland ZIP codes

Sun, 31 May 2020 03:24:47 +0000

A publicly-available MD COVID-19 metrics that I didn’t investigate much is cases per ZIP code. I created a dashboard where you can highlight one zip code at a time. Tyler Fogarty built a cool Treemap Explorer. Silver Chips has a nice heatmap of all zip codes as part of their extensive dashboard (a bit like the MDH dashboard). How can we make sense of all this?

A classical way to see it is to look at the daily number of positive cases, similarly to what I did for counties or the state.

Will it be the end of Stage 1 in Maryland?

Sat, 30 May 2020 21:00:18 +0000

Since May 14, 2020, Maryland is carefully reopening from an easy lock-down caused by coronavirus spreading thru the community (and all over the world). In this post, I’ll go through all the variables we have on the MD Health Department dashboard. But first, the official data comes from the MD dashboard and if you want scientific information about COVID-19, please consult the CDC website. If you are interested, you can read my previous posts on COVID-19 in Maryland from this page.

No visible impact yet of different COVID-19 Stage 1 strategies in Maryland

Thu, 21 May 2020 06:25:25 +0000

In my previous post, I was wondering if Maryland was ready to reopen, ready to enter Stage 1 of COVID-19 recovery. I also mentioned, in the end, that if Gov. Hogan announced the reopening of Maryland, he also gave counties the power to “fully” open, to be partially open or even to remain closed. You can see more info about Maryland Strong: Roadmap to Recovery: there is a map of what Counties decided.

MD counties COVID-19-specific death rate

Sun, 17 May 2020 02:32:22 +0000

Since a few weeks, I report the raw number of COVID-19 deaths in Maryland counties. If this gives an idea of the cumulative number of deaths - which is interesting - it doesn’t reflect the fact that some counties have more inhabitants than others. That’s why I plotted below the number of COVID-19 deaths adjusted for the population (i.e. the COVID-19-specific death rate):

Today (May 16, 2020), in terms of absolute number of deaths, Montgomery, Prince Georges and Baltimore County are the top 3 counties (this is the same for cases but not in the same order). In terms of confirmed deaths per 100,000 population, the top 3 counties are Kent, Prince Georges and Montgomery.

MD counties COVID-19 cases adjusted for population

Tue, 12 May 2020 04:42:23 +0000

Since a few weeks, I report the raw number of COVID-19 cases in Maryland counties. If this gives an idea of the cumulative number of cases - which is interesting - it doesn’t reflect the fact that some counties have more inhabitants than others. That’s why I plotted below the number of COVID-19 cases adjusted for the population:

Evolution of COVID-19 confirmed cases in Maryland counties, adjusted and not adjusted for population, on May 11, 2020

Trend in Coronavirus cases in Maryland (3)

Mon, 27 Apr 2020 16:12:00 +0000

Following up on my two previous posts ( here and here), I am writing a third post on COVID-19 in Maryland because I believe we enter a new phase.

Before continuing, please note that the same disclaimer as in my previous post applies here (in short: read the CDC and MDH websites for official information).

In the first phase, the importance was to detect and make sure COVID-19 patients were treated (also: make sure not to overwhelm the healthcare system, flatten the curve, lower the baseline, & stay at home!). My two previous posts were following these efforts, thanks to daily data released by the Maryland Department of Health (MDH) on its dashboard. My second post will still be updated with the latest data from there, go read it!

Trend in COVID-19 cases by Zip code in Maryland

Mon, 27 Apr 2020 00:43:35 +0000

Since the Maryland Department of Health (MDH) started to display number of COVID-19 cases for each Zip code in its dashboard, I was wondering how to display this information in a nice way. The MDH display the information as a map - very nice but it lacks from where each Zip code came from: is the number of cases increasing or decreasing?

Following on my busy chart with the evolution of all Zip codes (and highlighting just one of them - that may not be the one you are interested in, see previous post), I created a simple dashboard where you can select the Zip code you are interested in and see how cases are evolving. You can play with it here: https://jepoirrier.shinyapps.io/md-coronavirus-zip-app/ (screenshot below). Enjoy!

Trend in Coronavirus cases in Maryland, USA (2)

Sun, 29 Mar 2020 03:12:18 +0000

This post was last updated on April 26, 2020.
A new post from April 27, 2020 is here.

Following up on my previous post, here are updated trends in Coronavirus cases in Maryland (USA), the state I live in. I am writing a second post because the Maryland Department of Health (MDH) updated its dashboard with way more data than before (more on this below). Before continuing, please note that the same disclaimer as in my previous post applies here (in short: read the CDC and MDH websites for official information).

Trend in Coronavirus cases in Maryland, USA

Mon, 16 Mar 2020 23:17:29 +0000

Disclaimer: Although I work in infectious diseases, I’m not a specialist in Coronavirus. For the most up-to-date information on Coronavirus in the US, please visit the CDC website. For the most up-to-date information on Coronavirus in Maryland, please visit the Maryland Department of Health. That being said, now you can proceed at your own risk ;-)

This post was updated by one post on March 28 and another one here on April 27. Read the latest one here.

283 tweets about flu today

Wed, 14 Nov 2018 05:01:54 +0000

I wanted to use the TwitteR package for R since a long time, I tried but didn’t do much of it. Today I found a few minutes, followed simple recipes (I admit), and looked at the number of tweets about flu today (November 13, 2018). Result: 283 tweets in English (I wanted to focus on the USA but, for some reason, I couldn’t … yet!). That’s not a lot. But remember we are only at the beginning of the influenza season 2018-2019 in the Northern hemisphere.

Time commuting in Belgium

Mon, 06 Aug 2018 18:41:19 +0000

DISO1 - Data I Sit On, episode 1. This post is the first of a series of a few exploring data I collected in the past and that I found interesting to look at again … (I already posted about data I collected, see the Quantified Self tag on this blog)

Life is short and full of different experiences. One of the experiences I don’t specifically enjoy but is integral part of life is commuting. Although I tried to minimize commuting (mainly by choosing home close to the office) and benefit(ed) from good work conditions (flexible working hours, home working, etc.), a big change occurred when I took a new opportunity, in 2015, to work in the Belgian capital, Brussels.

Increasing certainty in flu vaccine effectiveness

Fri, 23 Feb 2018 16:48:18 +0000

According to CDC data, studies are getting better at estimating the influenza vaccine effectiveness.

With the 2017-2018 flu season still going on in the USA, there are already some indication that vaccines have some effectiveness (although its target strains were mismatched). The CDC reports how it measures vaccine effectiveness here and I was interested in their confidence intervals (the interval that takes into account uncertainties to extrapolate to the broader, unknown population).

Euthanasia in the Netherlands and Belgium, 1990-2015

Fri, 18 Aug 2017 23:24:59 +0000

While parsing the general literature, I found this paper from van der Heide et al. (2017) giving some numbers about end-of-life decisions in the Netherlands these past 25 years. I was wondering if one could see similar evolution in Belgium. And I didn’t have to look very far: van der Heide cited another NEJM paper with Belgian numbers ( Chambaere et al., 2015 ; an attentive reader will notice “Belgian” data is “only” about Flanders, not the whole Belgium).

Activity tracker: waist vs. wrist

Thu, 17 Aug 2017 16:03:36 +0000

A few weekends ago, I was challenged by a friend to do more steps than him. Of course, I won ;-) But I noticed he was wearing his activity tracker on his wrist while I was wearing mine on my waist. As I noticed several times before, when I had an activity tracker on my wrist, these devices tend to capture some movements even if you don’t actually walk (while typing energetically on the computer or while driving for instance).

So I took the opportunity of a small trip to wear 2 activity trackers, one Fitbit One on my waist and one Fitbit Charge HR on my wrist.

Counting steps is the easiest way to reduce cardiovascular risk

Thu, 16 Feb 2017 01:42:00 +0000

After abandoning my Fitbit device in January because using it didn’t see improvement in my weight (see previous post), I was wondering if I could still measure my risk to develop cardiovascular diseases and other preventable chronic diseases (diabetes e.g.). So, still sitting at my desk (something I do for more than 8 hours a day in theory - probably more in practice), I looked into the ways to monitor my risk for these diseases …

Evolution of the number and causes of death in Belgium (2010-2014)

Fri, 20 Jan 2017 01:37:18 +0000

Statbel, the Belgian governmental organisation for data and statistics, just released mortality data for 2014 ( press release in French, dataset). The headline of their press release was that, for the first time, tumors were the first cause of death for Belgian men. Diseases of the circulatory system remains the main cause of death in Belgium, for women and for both sex together.

While the death of someone is a bad news in itself, I’m more interested here in the evolution of death causes. I’m interested in the evolution of causes of death because it might be a consequence of the evolution of the Belgian society and, as a proxy, of any (most) developed, occidental countries.

About antibiotic resistance and the price of drugs

Fri, 20 May 2016 18:09:00 +0000

Many headlines stated today that UK wants to tax pharmaceutical companies again in order to contribute to a pooled fund against antimicrobial resistance (AMR). The proposed ‘pay or play’ mechanism is a bit more subtle than that. The report ( full text here) is also suggesting other financing mechanisms (including the improvement of existing ones) as well as describing potential non-financial measures to reduce these resistances in the first place. Actually, financial measures occupy only about 6% of the report. But headlines need to be catchy. Let’s see a broader picture on tackling antibiotic resistance …

Is it worth buying a coffee machine at work?

Tue, 15 Mar 2016 17:57:52 +0000

As I moved to a new office, I met new colleagues and one of them brought her own coffee machine and placed it on her desk. It’s a bright red Nespresso machine, a kind of statement that the owner doesn’t drink the free coffee offered in kitchenettes on all floors:

Given that the company has a professional Nespresso machine downstairs (i.e. similar quality of coffee but with capsules of different shapes), I was wondering if this is really worth buying. The calculation is simple …

Apple HealthKit already created some disruptions ...

Sat, 19 Sep 2015 23:45:33 +0000

… At least in the minds of people.

Marketing is a powerful persuasion tool and you sometimes need a few early applications to create the impression that something radically new came and is changing an area.

I like to listen to podcast while doing repetitive activities that don’t require my brain too much. One of the podcasts I listen to is the Clinical Air from the Pharma Talk serie. A few weeks ago, I listened to episode #14 about consumer electronics in clinical research. It was all about the Apple HealthKit. In a sense it was very interesting to hear about it as it contained more details than its Wikipedia page for the moment ; another top-level summary of its capabilities is found in this Rahlyn Gossen’s blog post (Rahlyn was one of the guests of this episode). Episode #14 was published on July 21, 2015.

Movember 2014 is over, thanks for your support!

Fri, 12 Dec 2014 00:14:20 +0000

With more than 2,400€ collected, our team - Bordet’s angels - can be proud, for a first participation! We are 12th of more than 100 Belgian teams. One key learning is that the gold, old paper display still works better than anything else to raise money.

And it was fun for me, a bit itchy in the end. But with the right trimming tools, this goes away very quickly. Thanks for all my supporters ;-) - your support is worth a thousand thank-you!

Nearly halfway through Movember

Wed, 12 Nov 2014 23:42:38 +0000

We’re nearly halfway through Movember, the month we grow our moustache in order to raise awareness about men’s health. I am in Amsterdam, for a congress and this was the hardest day of the month so far: since 8am, nearly every single person I met said it didn’t look good. And this can be harsh when you talk with (potential) business partners! However, practically, when you have time, this is an unique opportunity to initiate discussions with others about prostate cancer.

Polio eradication geographical modelling

Mon, 07 Jul 2014 16:41:00 +0000

I recently read with interest Dr. Gammino’s post on how geospatial data and microplanning is helping the CDC and its partners to work towards the eradication of polio.

There Dr. Gammino describes the hurdles faced by healthcare workers in countries where census data is often missing, where political, seasonal and geographical variations are making these more difficult. The description of the different social structures in urban or rural areas was also interesting. But the post also highlights how “social mapping” and geographic information systems (GIS) are helping understanding where the population resides and helping reaching them (here for polio vaccination but this could be for other purposes: maternity care, child care, etc.).

2013 in review: how to use your users' collected data

Sun, 19 Jan 2014 11:11:56 +0000

With a few days of interval I received two very different ways of reviewing data collected by users of “activity trackers”.

The first one came from Jawbone (although I don’t own the UP, I might have subscribed to one of their mailing-lists earlier) and is also publicly available here. Named “2013, the big sleep” it a kind of infographics of how public (and mostly American) events influenced sleep of the “UP Community”. Here data about all (or at least a lot of) UP users were aggregated and shown. This is Big Data! This is a wonderful and quantitative insight on the impact of public event on sleep! But this is also a public display of (aggregated) individual data (something that UP users most probably agreed by default when accepting the policy, sometimes when they first used their device).

More sleep with Fitbits

Wed, 08 Jan 2014 21:05:58 +0000

After a bit less than 2 hours, jepsfitbitapp retrieved my sleep data from Fitbit for the whole 2013 ( read previous post for the why (*)). Since this dataset covers the period I didn’t have a tracking device and, more broadly, I always slept at least a little bit at night, I removed all data point where it indicates I didn’t sleep.

So I slept 5 hours and 37 minutes on average in 2013 with one very short night of 92 minutes and one very nice night of 12 hours and 44 minutes. Fitbits devices do not detect when you go to sleep and when you wake up: you have to tell tem (for instance by tapping 5 times on the Flex) that you go to sleep or you wake up (by the way this is a very clever way to use the Flex that has no button). Once told you are in bed the Flex manages to determine the number of minutes to fall asleep, after wakeup, asleep, awake, … The duration mentioned here is the real duration the Fitbit device considers I sleep (variable minutesAsleep).

Getting some sleep out of Fitbits

Sun, 05 Jan 2014 00:11:21 +0000

After previous posts playing with Fitbit API ( part 1, part 2) I stumbled upon something a bit harder for sleep …

Previous data belong to the “activities” category. In this category it is easy to get data about a specific activity over several days in one request. All parameters related to sleep are not in the same category and I couldn’t find a way to get all the sleep durations (for instance) in one query (*). So I updated the code to requests all sleep parameters for each and every day of 2013 … and I hit the limit of 150 requests per hours.

Do you climb more floors when moving from an apartment to a house?

Wed, 25 Dec 2013 22:47:08 +0000

I continue to explore data about my physical activity in 2013 ( see part 1). We moved from an apartment (on the third floor of a building) to a house (with two floors) on July 1st, 2013. I was wondering if the change would have an impact on the number of floors I climbed: I now have to climb to reach bedrooms and go down to go in the living room. A standard house.

2013 with Fitbits

Mon, 23 Dec 2013 23:22:46 +0000

2013 is near its end and it’s time to see what happened during the last 360 days or so. Many things happened (graduated from MBA, new house, holidays, ill a few days, …) but I wanted to know if one could quantify these changes and how these changes would impact my daily physical activity.

For that purpose I bought a Fitbit One in March 2013. I chose Fitbit over other devices available because of the price (99 USD at the time) and because it was available in Europe (via a Dutch vendor). At that time the Jawbone Up was unavailable (even in the USA) and the Nike Fuelband couldn’t track my sleep.

Belgium doesn't score well in the Open Data Index (not speaking about health!)

Mon, 11 Nov 2013 23:00:35 +0000

The Open Knowledge Foundation (OKF) released the Open Data Index, along with details on how their methodology. The index contains 70 countries, with UK having the best score and Cyprus the worst score. In fact the first places are trusted by the UK, the USA and the Northern European countries (Denmark, Norway, Finland, Sweden).

And Belgium? Well, Belgium did not score very well: 265 / 1,000. The figure below shows its aggregated score (with green: yes, red: no, blue: unsure).

Map of GAVI eligible countries in R

Sun, 10 Feb 2013 22:48:45 +0000

I was trying to reproduce the map of the GAVI Alliance eligible countries (btw I was surprised India is eligible - but that’s the beauty of relying on numbers only and not assumptions) in R. This is the original map (there are 57 countries eligible):

I started to use the R package rworldmap because it seemed the most appropriate for this task. Everything went fine. Most of the time was spent converting the list of countries from plain English to plain “ISO3” code as required (ISO3 is in fact ISO 3166-1 alpha-3). I took my source from Wikipedia.

Today is world diabetes day (Merck ends MK-0431E)

Wed, 14 Nov 2012 09:34:38 +0000

As WHO and other organisations are celebrating World Diabetes Day (WDD) it is always sad to read that a new potential drug is stopped.

This time Merck & co. stopped the clinical trial MK-0431E studying the co-administration of Sitagliptin and Atorvastatin in inadequately controlled Type 2 Diabetes Mellitus. Merck cites “business reasons” without further explanations.

Sitagliptin is sold under the trade name Januvia. It is an oral antihyperglycemic and one of the (if not the) best selling product of Merck with US$975 million revenue in the third quarter of 2012. On the other hand Atorvastatin is a statin lowering blood cholesterol. It was a blockbuster for Pfizer (sold under the trade name of Lipitor) until its patent expired.

Happy Halloween! (Pharma Q3 results and job losses so far)

Thu, 01 Nov 2012 09:58:19 +0000

Happy Halloween! It’s the season for Q3 reports a bit everywhere so also in Pharma: Abbott (↑), Elan (↑), Eli Lilly (↓), Bristol-Myers Squibb (↓), Sanofi (↓), Novartis (↓), Shire (↑), AstraZeneca (↓), Merck & Co (↑), Novo Nordisk (↑), GlaxoSmithKline (↓), …

Idea shared #2 - the feedback toothbrush

Mon, 22 Oct 2012 21:26:28 +0000

After the T-shirt that measures your sleep better than an app, here is idea #2: the toothbrush that provides some feedback.

The idea is simple - so simple it was already applied elsewhere. The idea is to provide feedback about the quality of the way people brush their teeth. The Brushduino focuses on entertaining kids to keep them brushing at the right place for the right amount of time. Other projects (with many variants) focus specifically on time spent brushing.

Idea shared #1 - measure your sleep

Sat, 22 Sep 2012 21:48:32 +0000

I don’t consider having more or better ideas than others. But I gradually realized I have less and less time for some activities like programming, electronics etc. Maybe that’s how we realize we are getting older now adults. So I decided to share these ideas rather than fueling the illusory idea that I will implement them one day.

So idea 1 is about measuring sleep. I recorded animals’sleep during my Ph.D. - but it was thanks to an EEG device. I think that if you want to understand or improve something you have to first measure it in a way or another. So I started to try to measure my own sleep with an app ( Sleep Cycle). But despite its good reviews it doesn’t work, at least for me.

Forget pills, here comes e-pills!

Wed, 15 Aug 2012 21:40:32 +0000

The US FDA recently approved Proteus Digital Health Ingestion Event Marker ( IEM). Basically, it’s a pill with some electronics attached (very tiny electronics: around 0.5mm in diameter for a total weigth of 5mg, see picture below). Once activated the pill transmit a signal and, coupled with a detector, you know when the pill got into your body.

Edible sensor for electronically confirming adherence to oral medications.

Effects of Tobacco on health - visualized

Tue, 17 Jul 2012 00:49:16 +0000

As you probably know I am interested in both diseases (and health in general) as well as visualization. Recently Online Nursing Programs (*) invited me to have a look at their latest infographics about the effects of tobacco on health ( directly to figure).

Although numbers seem correct (references are at the bottom), although they intelligently re-use the presentation of some well-known tobacco companies, there is one thing that I don’t like that much: like this sentence, the figure is very, very long. You have to scroll many pages in order to see everything. It may look like a story but it is not presented as such (I mean: there are no clear marks of different steps in the story, except the three “chapters”). On the right is the complete figure in exactly 800 pixels of height - can you read something? GOOD.is solved this issue by using a Flash player that allows the viewer to woom in/out and go to different sections of the figure ( see here for instance).

Eat meat or not?

Sun, 22 Apr 2012 21:21:18 +0000

It all started with a strong statement in the LA Times:

If early humans had been vegans we might all still be living in caves.

It says nothing and everything at the same time … Not eating meat would have stopped our “evolution” from early humans? Not eating meat would make us dumber? Or does it have something else to do? It does.

Pi in Pubmed

Mon, 19 Mar 2012 18:06:37 +0000

On March 14th, 2012 (3/14/2012), it was Pi day. According to Wikipedia, Pi (π) is a mathematical constant that is the ratio of any Euclidean circle’s circumference to its diameter. While others estimated π using Monte Carlo in R or declared π is wrong, I tried to see how many times the pi value is cited in Pubmed, a database of references and abstracts on life sciences and biomedical topics. And here are the results (please note the log y-axis):

Projection of the American ageing population

Fri, 06 Jan 2012 22:20:15 +0000

Yesterday, GOOD issued an infographic of America’s Aging Workforce (reproduced below). One of the key learning I take from it is that many Americans are unprepared for retirement. Indeed, the average American worker has saved $25,000 for retirement but it is estimated she/he will need $350,000 if she/he wishes to retire at 65 (i.e. 14 times more money!).

I was also wondering: after China and Belgium, how will the population age in the USA?

2012 will be the first year after the International Year of Chemistry

Fri, 06 Jan 2012 20:31:49 +0000

Indeed: 2011 was the International Year of Chemistry (IYC). But why IUPAC and UNESCO dedicated a year to that basic science? It was for two reasons: one looking at the past and one looking at the future.

Looking at the past, 2011 was the 100th anniversary of Marie Curie’s Nobel Prize in Chemistry for her discovery of the elements radium and polonium. She was the first woman to be awarded a Nobel Prize. And her discovery was very important for both the science in itself and its applications to health. Radium’s radioactivity seemed to contradict the principle of the conservation of energy. The discovery of radium allowed other great names in chemistry and physics like Rutherford to study the atom and radioactivity decay. In medicine, the radioactivity of radium allowed the development of radiation therapies, used to control or kill malignant cells in cancer treatment.

Health talks at TEDxBrussels

Sun, 27 Nov 2011 22:09:28 +0000

When I wrote my last post, videos of health talks at TEDxBrussels were not out yet. Now they are and you can watch them below …

First Andrew Hessel started by talking about synthetic biology, biotechnologies and his participation in the open source biology movement. One day, there will be an org (organism) for the things you want to do.

[youtube=http://www.youtube.com/watch?v=oQtyRzP7SUg]

Then Jack Tiszynski followed with the drastic idea of replacing doctors by software for diagnostics and brought the idea that we will have a “virtual double” in our future smartphones. This double will know our predisposition to diseases and suggest prevention methods and cures.

TEDxBrussels in tweets and videos

Wed, 23 Nov 2011 23:10:57 +0000

TEDxBrussels is a local, self-organized event that brings a TED-like experience to Brussels. I already often mentioned videos and presentations from TED (for instance here, here or here). When I read that it will again be organized in Brussels in 2011 I decided to attend this edition. Here is a short summary of this intense day with my tweets and the just-released videos. It would be very time consuming to write about each and every talk. Here I will just highlight speakers I like the most (you can have a look at TEDxBrussels website for the complete list of speakers).

Visualizing how a population grows to 7 billion (NPR)

Wed, 02 Nov 2011 22:59:03 +0000

The NPR has produced a nice visualization / video showing how population grew to 7 billion ( original article):

[youtube=http://www.youtube.com/watch?v=VcSX4ytEfcE]

If you want to model the improvement in child survival, you just turn the birth tap off (or nearly). Then, with wealth, prevention, healthcare and better food, the population will also grow older (death tap also turned off or nearly) and during a certain time, lots of adults will be economically active (i.e. they will work and consume). This is a demographic dividend. But it comes with a risk: at the next stage, there might be a disproportionately high number of people compared to / depending on a small number of active adults (the next generation). In addition, if you fill it up slowly but you also empty it slowly, the container risk to be full soon, it all depends on the various rates …

Human Development Index 2011

Wed, 02 Nov 2011 22:23:18 +0000

The United Nations Development Programme (UNDP) released its Human Development Report 2011. It " argues that the urgent global challenges of sustainability and equity must be addressed together – and identifies policies on the national and global level that could spur mutually reinforcing progress towards these interlinked goals".

In this report, there is a ranking, the Human Development Index (HDI). The HDI is a way to measure the development. It combines indicators in three main dimensions: health, education and living standards. The mathematical way used to combine these indicators is explained in a technical note (PDF). The interest is of course to have a single number to use in comparison for both social and economic development. It’s not the only element to take into account to compare development. It’s merely a starting point giving an overview of development. An in-depth discussion about development and comparison between countries will need to go further and analyze each indicator separately (as well as other indicators if possible).

How to feed 7 billion people?

Tue, 01 Nov 2011 00:03:56 +0000

The world reached a population of 7 billion people at the end of October 2011. United Nations symbolically chose Danica May Camacho, a girl born in Philippine, to mark this global population milestone. I recently wrote about the world population getting older, about non communicable diseases becoming the most dangerous threat to health ( here too) or about World Population Day(11th of July 2011). We are now 7 billion and new projections tells us we will be 9.3 billion in 2050. When I heard all the news around this, I couldn’t help but think about Hans Rosling’s presentation on population growth at TED Cannes, in 2010.

First promising results for a malaria vaccine

Tue, 18 Oct 2011 21:45:16 +0000

Malaria is the 5th cause of death in low-income countries ( according to WHO). That’s why I’m very happy to read that a malaria vaccine showed promising results in a phase 3 clinical trial (in The Guardian, The New York Times or Google News). As usual, I find very interesting to get all the information at the source: the original scientific paper was just published in The New England Journal of Medicine.

Yesterday was International Day of Older Persons

Sun, 02 Oct 2011 12:32:35 +0000

On 14 December 1990, the United Nations General Assembly designated 1st of October the International Day of Older Persons. 1990 … it is already more than 20 years ago! People who signed the resolution at that time are now more than 20 years older. Some (most) of them probably are now considered as “old persons”. Do they still have the same view on elderly? Maybe the highlighted principles at that time (independence, participation, care, self-fulfilment, dignity, …) are too broad, too short, just enough?

NCDs account for the majority of deaths worldwide

Sat, 01 Oct 2011 22:15:59 +0000

A few days before my last post and still about the UN High Level Meeting on Prevention and Control of Non-communicable Diseases, The Economist issued a daily chart showing that non-communicable diseases (NCDs) account for the majority of deaths worldwide. I copy the chart below:

[caption id=“attachment_1115” align=“aligncenter” width=“497” caption=“The Economist: non-communicable diseases account for the majority of deaths worldwide”] [/caption]

The state of non communicable diseases

Wed, 28 Sep 2011 18:45:51 +0000

Last week, United Nations gathered in New York, USA, to talk about prevention and control of non-communicable diseases (NCDs). Non-communicable diseases are non-infectious, of long duration and generally progressing slowly. Due to the fact they are not infectious, there is no pathogen to target and there is no transmission medium to fight. Due to their long duration and slow progression, one usually notices NCDs when it’s too late and eradicating NCDs is less spectacular than other (not less important) infectious diseases. However WHO measured that NCDs represents more than 60% of all deaths in the world. For the occasion, WHO released an introductory video that summarize the issue.

OS need an immune system and not a CDC-like

Sat, 23 Jul 2011 01:15:30 +0000

In an IT World article, Tom Henderson gives many details about a US-government-led CDC-like organisation to fight malware. In summary, he states that companies and consultants providing security and prevention around operating systems don’t have any real motivation to eradicate malware. And in case of an “outbreak” of these malware, he added one needs a US government body to look after every computer “health”, coordinate the surveillance and the response. He even pushes the comparison with the human medical system by introducing a Hippocratic Oath for computer healthcare.

Today is World Population Day

Sun, 10 Jul 2011 22:03:59 +0000

Today, 11th of July 2011, is World Population Day. For that occasion, and as the world population is expected to surpass 7 billion this year, the UNFPA is launching a new campaign: 7 billion people - 7 billion actions.

They highlight 7 key issues to explore:

Poverty and inequality: reducing poverty and inequality also slows population growth.
Women and girls: unleashing the power of women and girls will accelerate progress on all fronts.
Young people: energetic and open to new technologies, history’s largest and most interconnected population of young people is transforming global politics and culture.
Reproductive health and rights: ensuring that every child is wanted and every childbirth safe leads to smaller and stronger families.
Environment: all 7 billion of us, and those who will follow, depend on the health of our planet.
Ageing: lower fertility and longer lives add up to a new challenge worldwide: providing for aging populations.
Urbanization: the next two billion people will live in cities, so we need to plan for them now.

These issues are not new. They are not even original: most bodies or meetings looking at issues for the future have approximately the same issues. But at least it’s another initiative to raise awareness, to think about them. And, most importantly, to act to tackle them.

Sometimes people are really stupid

Sun, 10 Jul 2011 21:17:45 +0000

I just read that orange agent is used in Brazil to clear the Amazon. I am not judging people who may be forced by their living conditions to do this (although I doubt people who did this are poor since they sprayed it by plane). It may be the cheapest way to clear a forest to use the land for pasture (although I doubt buying chemical and spraying it by plane is cheap). But …

The Top 5 Killers of Men

Sun, 26 Jun 2011 18:08:22 +0000

From Delicious, I saw that Yahoo had an article about the top 5 killers of men. I thought it would be nice to see from where they get there data.

First, I have to mention that the article is really about American men, nothing else (not about mankind, not about men around the world, not about women, children, etc.). The article is related to the US National Men’s Health Week (the US National Women’s Health Week was in May 8-14, 2011). Although the article is giving advices, there are no sources of information.

March 24th was world TB day

Tue, 29 Mar 2011 21:35:24 +0000

TB stands for tuberculosis. It’s an infectious bacterial disease caused by Mycobacterium tuberculosis, which most commonly affects the lungs. It is transmitted from person to person via droplets from the throat and lungs of people with the active respiratory disease.

Like all other World Days regarding infectious diseases, it is meant to raise awareness about its global epidemiological aspects and the efforts to eliminate it. For tuberculosis, March 24th was chosen because Robert Koch first described Mycobacterium tuberculosis on March 24th, 1882. He then received the Nobel Prize in Physiology or Medicine for this in 1905.

Today is not World Epilepsy Day

Mon, 14 Feb 2011 22:15:00 +0000

I continue in the serie of “World x Day” and for a reason still unknown even to myself, I thought today was the World Epilepsy Day (it’s in fact on March 26th, called Purple Day). But, anyway, epilepsy is “a common chronic neurological disorder characterized by seizures. […] Epilepsy is usually controlled, but cannot be cured with medication, although surgery may be considered in difficult cases.” ( Wikipedia).

Out of curiosity, I was looking for mathematical models for the description of the epidemiology of epilepsy. But unfortunately, I couldn’t find anything. Probably because epilepsy is not an infectious disease for which tentative mathematical models have more predictive power (in terms of the population scale and time scale). The epidemiology of noninfectious diseases is primarily a study of risk factors associated with the chance of developing the disease. Nothing very fancy for a mathemarical model! ;-) (But if you find something, feel free to share! Thanks in advance!)

World Cancer Day

Sun, 06 Feb 2011 21:09:13 +0000

It doesn’t seem jolly but last Friday, it was the World Cancer Day. About this, the WHO set up a nice website about cancer control.

Following my previous post on Jamie Oliver and the top 15 causes of death in the USA, I started to collect similar data from other countries. Linking this to cancers, the annual statistics on cancers in Belgium can be found on the Belgian Cancer Registry. The latest numbers are however from 2006. Here are the top 15 cancers in Belgium in 2006 (all sexes and regions mixed):

World Leprosy Day

Sun, 30 Jan 2011 22:18:57 +0000

Today was World Leprosy Day. Leprosy has a high incidence in countries like India, Brazil and Burma (and other countries in the middle of Africa). But its incidence in occidental countries is rather low. This may explain why there isn’t a lot of [epidemiological models of leprosy](http://www.ncbi.nlm.nih.gov/pubmed?term=leprosy epidemiological model) (I wish I had some time for this kind of thing).