Tag Archives: reading

Reading in the lab

11 Jan

The winter break is a great opportunity to spend time in the lab with my students. One of the things we do, is read papers. Last week, we spent a morning reading the following paper:

Triple-Antiretroviral Prophylaxis to Prevent Mother-To-Child HIV Transmission through Breastfeeding—The Kisumu Breastfeeding Study, Kenya: A Clinical Trial. PLoS Medicine, 2011. Thomas , Masaba, Borkowf, et al. 

The paper shows that antiretroviral drugs taken by an HIV-infected mother help prevent transmission to the baby through breastfeeding. The reported rates of HIV infection of the infants during breastfeeding were less than half the previously reported rates from untreated women.

After everyone read the paper, and we all discussed it together, two students worked together to write an abstract and three students worked together to draw an abstract. Here are the results:

Abstract (by Kadie and Melissa)

The Kisumu Breastfeeding Study was a single-arm trial conducted with 522 HIV–infected pregnant women who took a triple antiretroviral regimen from 34 weeks of pregnancy to 6 months after delivery. The triple-ARV regimen consisted of zidovudine and lamivudine and either nevirapine or the protease inhibitor nelfinavir. The purpose of the study was to investigate how various ARV regimens given to mother and/or their infants affect mother to child transmission of HIV.

Data collected showed that between 0 and 24 months, the cumulative HIV transmission rate rose from 2.5% to 7.0%. The cumulative HIV transmission or death rate was 15.7%. Three percent of babies born to mothers with a low viral load were HIV-positive compared to 8.7% of babies born to mothers with a high viral load. Similarly, 8.4% of babies born to mothers with low baseline CD4 cell counts were HIV positive compared to 4.1% of babies born to mothers with high baseline CD4 cell counts. Although these findings are limited by the single-arm design, this study supports the idea that a simple triple-ARV regimen given to HIV-positive pregnant women regardless of their baseline CD4 cell count can reduce MTCT during pregnancy and breastfeeding in a resource-limited setting.

Graphical abstract (by Olivia, Patricia and Dasha)

2016-01-07 12.40.27


Some recommended and not-recommended science-related books

6 Jan

Last year I read some really cool books that are somehow related to my work. I also read books that were so annoying, I didn’t even finish them. I wanted to share some of my thoughts here.

Jim Ottaviani, Maris Wicks: Primates

Lovely comic book about three women researchers who study primates (Jane Goodall, Dian Fossey, and Biruté Galdikas). Great gift idea! Link to book


Steven Strogatz, The joy of X.

Highly recommended! Great book with essays about fun math. Made me want to learn more. Link to book.

Jennine Capó Crucet: Make Your Home Among Strangers

I very much enjoyed this novel about a young cuban woman who is the first of her family to go to college. It’s an easy read, but it has some insights that may be useful for those of us who teach. Link to book.

Vanessa Woods: Bonobo handshake

Well written memoire by traveler, writer and bonobo researcher Woods, with a lot of background on Congo and neighboring countries. The descriptions of awful violence during the wars in Congo may be upsetting to some. Link to book.

Bill Nye: Undeniable

The topic of this book, evolution, is dear to my heart, but I didn’t manage to finish it. It is simply not well written / edited. Link to book

Frank Ryan: Virolution

This book was definitely worse than Bill Nye’s book! It is not well written and it is full of nonsense about evolution. Disappointing, because it would have been nice to have a good popular book on viruses and evolution. Here Carl Zimmer explains why the book is not recommended: link to book review.





Four books I enjoyed reading before and after the birth of our baby

12 Jul

I love reading non-fiction books. Here are the books I most enjoyed reading before and after the birth of our baby

Month -2:  Ina May on natural child birth

This book helped me be confident that I could deliver a baby naturally.

I am not a hard core natural child birth proponent, but I was worried that giving birth in an American hospital would give me very high chances of a C-section even if that wasn’t medically necessary. A good friend sent me a wonderful book by midwife Ina May about natural childbirth. I mainly read the part of the book that consists of birth stories written by new mothers. It was inspiring and interesting, and it made me much more confident that I could deliver a baby. It also convinced me that biking and walking was good for me throughout my pregnancy.

Link to amazon

Month 0-3: The happy baby book

This book made taking care of our newborn less scary and less tiring.

The happy baby book (a gift from my cousin and her partner who are both psychologists) was extremely useful and really helped us to know how to soothe our baby. If you are too busy or tired to read, here is a synopsis: a baby likes to be in a swaddle (even if they may resist being swaddled), a baby likes to be held on their side or stomach, a baby likes sound (white noise, shushing), a baby likes to suck on something (finger, nipple, pacifier), and a baby likes little movements. Do all of those and likely the baby will calm down quickly. It definitely worked for our baby!

Link to amazon

Month 2-5: Working and pumping

This book brought support and advice when I went back to work and needed to pump milk.

When I went back to work, I was still breastfeeding my baby. This meant that I needed to pump breast milk at home and at work. We initially rented a pump from the hospital and then bought one (tip: call your insurance first, they usually pay if you buy through them).

Pumping milk is no fun, but a book I found in a second hand bookstore gave me a lot of information and motivation to keep doing it. The book is the story of a group of women who worked at IBM and who shared a room where they could go to pump during work hours. The women kept a notebook in this room, so that they could write to each other during their pumping sessions. They simply shared stories, frustrations, questions they had and helped each other with advice and support. Later, two of them wrote a book based on the notebook. The women in the book were so real and it almost gave me the feeling that I had friends who were going through the same thing as I was. I always kept the book with the pump and enjoyed reading a few pages during each pumping session.

Link to amazon

Month 6: Baby sign language book

This book convinced us to start learning sign language.

Intuitively, it makes a lot of sense to me that signing with babies is a good idea, but nothing is more convincing to a researcher like me than a randomized trial!

I enjoyed reading a book by Linda Acredolo and Susan Goodwyn, two researchers who pioneered baby sign language. Acredolo and Goodwyn did a randomized controlled trial to find out whether baby sign language had an effect on children’s development. They found that the kids who were taught to sign learned to speak earlier and used more complex sentences (Goodwyn et al 2000). Also they had a higher IQ at age 8 (12 pts difference, going from the 53rd to the 75th percentile, link). I don’t work in the field of child development, but my impression is that a 12 point gain (or 22 percentile points) in IQ is huge. As far as I know, the study has never been replicated, so maybe the real gain is not as big.

However, more important for my daily life is that I love learning sign language & signing with our baby! I have always been intrigued by sign language but I didn’t think I would ever learn a sign language. Now, our baby, who is 12 months old, can sign dog, daddy, flower, monkey, penguin, light, bird and car.

If you are curious, here is a nice video with a baby signing:

Link to amazon

Two dollars and a printed paper

20 Dec

I am one of those people who still reads articles on paper. In fact, I am not a very avid article reader. If I need to learn something new, I’d rather have someone explain it to me in person! Or I try to figure it out myself. For example, I prefer writing new code to reading the documentation of a software package (I agree, not very smart!).

 Making reading easierTwoDollarsAndAPaper

Obviously, not reading scientific literature is not a good idea. So I try to make reading as easy as possible for myself. And one of the things that works for me, is to print out one or two papers, and take them, with a pen and a couple of dollars, to a cafe, not far from my office. There, I order a coffee (the people who work in the Bytes cafe already know that I drink Americano), and I read the papers, while scribbling and drawing on them with the pen.


 The two big advantages of reading articles like this are:

1. Paper doesn’t have wifi, which greatly increases the probability that I will actually read. I am not even tempted to look up that one interesting reference in the first paragraph of the introduction (which could lead to another reference and another one until I am 2 hours further and still stuck in the introduction*).

2. I can write on the paper, which helps to read and remember what I read.

The two disadvantages of printing articles are:

1. Obviously, it costs paper, which is not very environmentally friendly.

2. I need to store the paper with the notes and be able to retrieve it, so that I don’t print the same paper twice (and make the same annotations twice).

NumberOnPaperSo where to keep paper copies of articles and how to find them back?

I use the following system.

1. Each paper gets a unique shelf number.

2. The number is stored in my Endnote library (Mendeley since a few weeks) with the reference so that I can see immediately whether I have the paper and where I can find it.

3. The paper is stored in a hanging folder ordered by number. The papers I read most recently are closest to my desk.

Simple, right?

Yes, it is quite simple, and this system has served me well since 1999 orso. I think I may have learned it from Jacqui Shykoff. But as far as I am aware, neither Endnote, nor Mendeley has a standard entry for “shelf number”. Why not? Am I the only one who keeps paper versions of articles? I once lost all my numbers when I moved from Endnote to Endnote on the Web (I paid a student to enter them again by hand!). And more recently, I postponed a switch to Mendeley because I thought I would lose the numbers again, but fortunately this didn’t happen.

Honestly, I don’t know how anyone can do without shelf numbers. Even if you keep your papers by alphabet or publication year, how do you know whether you have a paper version of an article? I know that this problem will cease to exist one day. When making notes on iPads becomes as easy as scribbling on a piece of paper. But until then, I will keep printing & drinking coffee as I read & filing the papers in my filing cabinets.

* In fact, this may be why I love reading scientific literature that is meant for a lay audience: it has fewer references.