The ridiculous order of the streets in the Excelsior (SF)

26 Sep

I live in the Excelsior neighborhood in San Francisco. My street is Athens Street. If I walk westwards from my home, I come to Vienna Street and then Naples, Edinburgh and Madrid. If you have any knowledge of map of Europe, you realize that the order makes no sense!

(Also, why is there Naples, but not Rome, and why Munich, but not Berlin? And why oh why, is there no Amsterdam Street? So many questions!)

Last week, I asked the students in the CoDE lab to create a map to show the ridiculous order of the streets in the Excelsior. They had fun figuring out how to make a map in R, so I thought I share their work here. Several students were involved, but my graduate student Olivia Pham did most of the work.

The code is here: http://rpubs.com/pleunipennings/212840

europe_excelsiormap

The surprising order of street names in the Excelsior neighborhood in San Francisco. We connected the cities in the order of the streets. London Street is the first city-name street if you enter the neighborhood from Mission Street, just east of London Street is Paris Street, then Lisbon Street etc. The last city-name street is Dublin Street which is closest to McLaren Park.

excelsiormap

A map of part of the Excelsior neighborhood showing the order of the city-name streets.

Successful experiment helps me sleep

5 Sep

A couple of weeks ago, I read about an experiment that showed that 100% of breastfed babies could learn to sleep through the night by eight weeks. I was skeptical, but also intrigued. My baby was eight weeks old then, and definitely not sleeping through the night. In case you are not familiar with baby sleep jargon: “sleeping through the night” usually means that a baby sleeps from before midnight till after 5AM. I think that midnight till 5AM is a very short night, but, hey, for a two-month old this is still pretty cool!

I decided to look up the original paper that described the experiment. Here is the link to the paper in case you want to read it too. The experiment was quite simple. The researchers recruited 26 first-time parents to participate in a baby sleep study. All of them were planning to exclusively breastfeed the baby until at least eight weeks. 13 families were put (at random) in the control group and 13 were put in the experimental group.

Simple instructions for the experimental group

Both groups of parents were asked to keep detailed 72 hour diaries once a week for eight weeks, in which they recorded when their baby slept, when it nursed and how much milk it consumed at each feed*.

In addition, the parents in the experimental group were told to do the following:

1. Always feed the baby between 10PM and midnight (focal feed).
2. Try not to hold, rock or nurse the baby to sleep.
3. Accentuate the difference between day and night.
4. Make sure the baby is really crying before picking them up (and do not pick them up when they only whimper).

At three weeks, if the baby was growing well, the following instruction was added:
5. If the baby wakes up and cries between midnight and 5AM, try reswaddling, patting, diapering and walking. Only if after trying these things the baby is still crying, offer a feed.

It worked for the babies in the study!

The results were very clear. The babies in the experimental group learned to sleep through the night. When they were eight weeks old, all 13 babies in the experimental group (100%) slept through the night at least two nights of the three nights that the sleep diaries covered. This was true for only three out of 13 babies in the control group (23%). The researchers found no differences in total milk intake or weight gain between the two groups.

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What I did

I was inspired by the clear results and the simple protocol that was used in the study. Other sleep-through-the-night plans I had previously read about included very strict day-time routines, which I didn’t want to stick to. So I decided to try to follow the protocol for a few weeks. I already didn’t hold or nurse the baby to sleep and the day-night difference was clear – so I made no changes there. I now added the focal feed between 10PM and midnight and if the baby woke up, I tried reswaddling, a new diaper and a bit of walking before I offered the little one a feed. I also tried to wait until the baby was really crying before picking her up, but I found this very hard, and I wasn’t very consistent with it. Also, some nights I was very tired, and I gave in quickly, and simply nursed the baby so that I could get back to sleep**.

And it worked for my baby too!

I started just before our baby was eight weeks old. After a week, I noticed that she was sleeping longer stretches and after three weeks, she started sleeping through the night consistently. She has done several nights of eight hours already (she gets her night feed at 10PM and sleeps till 6AM). I am stoked! I had no idea that this was possible, and it wasn’t even hard!
Thank you Dr Teresa Pinilla and Dr Leann L. Birch for writing that paper 23 years ago! If I manage to write a paper this semester, it will be thanks to you!

*To find out how much milk a breastfed baby drinks, the baby can be weighed before and after the feeding.
** This may sound like I was doing everything by myself, and that was only true at night. During the day my husband did the laundry, the cooking, the grocery shopping and most of the care for our toddler.

 

The acknowledgement section of our NSF proposal

25 Aug

A few weeks ago two colleagues and I submitted an NSF proposal. We submitted on a Friday afternoon even though the deadline wasn’t until Tuesday! I am proud that we managed this almost without any deadline stress!

I had fun and we wrote a great proposal

I know that we may not end up getting funded by NSF, but until we get that message, I plan to be very optimistic. We wrote a really neat proposal for a great project. I can’t wait to get started! The ambitious goal of the project is to determine the fitness cost of every possible point mutation in the HIV genome in vivo.

I think nobody likes to write proposals when the success rate is only 5%, but I actually enjoyed working on this proposal and I learned a lot while writing it: both about the biology of our project and about the art of proposal writing. It’s important for me to commit that to paper (OK, screen) so that if NSF decides not to fund us, I will remember that writing the proposal was actually a good experience.

Writing with a newborn

In addition the many scientists and administrators who contributed to the proposal, I also want to mention how I could write a proposal with a newborn. We started working on the proposal two weeks before I gave birth and we submitted the proposal when our baby was just shy of seven weeks old. The hours that I spent on the proposal were made possible by my mom who flew in to help and by the fact that Facebook gives new parents four months paid paternity leave so that my husband was also at home during my maternity leave. It was fun to be home together with my husband and we took shifts working and taking care of Maya. Most days I worked on the proposal just two or three hours, so a large part of the work was done by others.

HomeOfficePleuni

Me in my home office with baby, changing table, a laptop and a grant writing handbook.

It was a huge team effort

Many people were involved in writing the proposal. Many more than I ever expected to be. I want to list them here so that I remember who helped out and also to show that being a researcher doesn’t have to be a lonely affair.

Note that these people are only the people I am aware off. Others certainly helped my co-PI Adi Stern.

The main team that wrote the proposal consisted of four people:

  • co-PI Adi Stern (Tel Aviv)
  • postdoc Marion Hartl (SFSU)
  • professional grant writer Kristin Harper
  • myself

At SFSU, people from the Office for Research and Sponsored Programs helped:

  • Rowena Manalo
  • Raman Paul
  • Michael Scott
  • Jessica Mankus
  • Uschi Simonis (vice-dean for Research)

At Stanford there were

  • co-PI Bob Shafer
  • collaborator David Katzenstein
  • Elizabeth White (Katzenstein lab)
  • Holly Osborne (Office for Sponsored Research)

In Tel Aviv

  • Office for Sponsored Research
  • Adi Stern’s lab members brainstormed ideas
  • Maoz Gelbart help with ideas and figures

Colleagues who read earlier versions of the proposal

  • Sarah Cobey (U Chicago)
  • Sarah Cohen (SFSU)
  • Alison Feder (Stanford)
  • Nandita Garud (UCSF)
  • Arbel Harpak (Stanford)
  • Joachim Hermisson (U Vienna)
  • Claus Wilke (U Texas Austin)

A huge thank you to all these amazing people! I am lucky to be part of such a supportive community.

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Is it a soft sweep or a hard sweep?

14 Aug

2016-08-14 11.49.34

As the summer and my maternity leave come to an end, I am starting to think about what I will do in the fall semester. One thing that is on my to do list is to write a review paper on soft sweeps together with Joachim Hermisson, who is spending the year at UC Berkeley. Joachim and I wrote three papers on soft sweeps ten years ago (H&P 2005, P&H 2006a and 2006b) and it’ll be fun to work together again.

One of the reasons that we are planning to write such a review paper is that in the last couple of years, some controversy has arisen surrounding soft sweeps. Put very simply, some people think that soft sweeps are ubiquitous and others think that they are nonsense.

Dmitri Petrov is a strong proponent of the view that soft sweeps are very common (Garud et al 2015, Messer and Petrov 2013). Jeffrey Jensen is probably the strongest critic of the concept of soft sweeps as evidenced by his paper entitled “On the unfounded enthusiasm for soft selective sweeps.” (Jensen 2014).

I look forward to writing a paper that makes the “It’s complicated” in the flowchart I made less complicated!

References

Garud, N. R., Messer, P. W., Buzbas, E. O., Petrov, D. A., Fay, J., Wyckoff, G., … Stephan, W. (2015). Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps. PLOS Genetics, 11(2), e1005004. doi:10.1371/journal.pgen.1005004

Hermisson, J., & Pennings, P. S. (2005). Soft sweeps: Molecular population genetics of adaptation from standing genetic variation. Genetics, 169(4), 2335–2352. doi:10.1534/genetics.104.036947

Jensen, J. D., (2014). On the unfounded enthusiasm for soft selective sweeps. Nature Communications, 5, 5281. doi:10.1038/ncomms6281

Messer, P. W., & Petrov, D. A. (2013). Population genomics of rapid adaptation by soft selective sweeps. Trends in Ecology & Evolution, 28(11), 659–669.

Pennings, P. S., & Hermisson, J. (2006a). Soft sweeps II-molecular population genetics of adaptation from recurrent mutation or migration. Molecular Biology and Evolution, 23(5), 1076–1084. doi:10.1093/molbev/msj117

Pennings, P. S., & Hermisson, J. (2006b). Soft sweeps III: The signature of positive selection from recurrent mutation. Plos Genetics, 2(12), 1998–2012. doi:10.1371/journal.pgen.0020186

 

 

 

 

Sometimes complaining helps

24 May

Two years ago I learned about a conference at Stanford called “Big Data in Biomedicine.” I was interested to sign up, but then found out that there were 40 male speakers and 2 women: not even 5%!

OK, I must admit that I was not entirely surprised, because large parts of Stanford are very male biased. But this seemed extreme even for Stanford. So I sent an email to the organizers and later learned that several others had done the same thing.

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And? It helped. People involved in the meeting realized that there was a problem and several women were added to the speaker list last minute for the 2014 conference.

Now, I just got an email about the 2016 conference and so I was curious to look at the list of speakers. They currently have 48 confirmed speakers and 20 of them are female. That is 42%!! Also, there is a few people of color on the list of speakers. Certainly not yet enough, but more than I usually see at these kinds of meetings.

I’d like to say: congrats to the organizers for creating an (almost) gender-balanced line-up and congrats to those of us at Stanford who opened our mouths. Complaining is not fun, and it’s not going to help us make friends or get ahead in our careers, but it can lead to change!

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Five Reasons why you should attend the Annual SACNAS National Conference

27 Apr

Guest post by: Bridget Hansen, SFSU undergraduate researcher

BridgetHansenPosterSACNAS2015

First, who am I? What is SACNAS?

My name is Bridget Hansen and I am an undergraduate in Microbiology at San Francisco State University, doing research at the Romberg Tiburon Center for Environmental Studies. Over the summer, I participated in the Howard Hughes Medical Institute Excellent Research Opportunity Program (HHMI-ExROP) summer research and the AMGEN program at the University of California, Berkeley. I worked on a project that I then presented at the SACNAS Conference this past October.

SACNAS stands for the Society for Advancing Chicanos/Hispanics and Native Americans in Science. This society, made up of many successful Chicanos and Native Americans in science related careers, puts on a national conference once a year. The conference has opportunities for scientists at all levels, from undergraduates to professors and researchers. Many graduate school recruiters and other professional organizations come to this conference to recruit, providing a great platform for networking.

I used this opportunity to network for graduate schools! I will be attending a PhD program in the fall, in part, thanks to my interactions that I had at SACNAS.

What happens at the SACNAS National Conference?

Students from all over the country submit abstracts for the opportunity to present their work, either in the form of a poster or an oral presentation. The students had a scheduled time and room to present. Other than presentations, the meat of the conference was geared towards guest speakers and networking. The whole goal of the conference was to introduce young students to the world of research and science related careers! The best part is the graduate student recruiter booths where you have the opportunity to chat with recruiters, professors, and students from that university.

Five reasons why I recommend SACNAS

  1. The networking

There were hundreds of booths set up, all stocked with professors, recruiters, graduate students and pamphlets listing the reasons why you should come to their school. Nearly every research institution was in attendance, looking for the next round of graduate students to apply to their programs. They want you to apply to their programs but most importantly, they want to make sure their school lines up with your research interests. You can ask them about the programs, the application process, what it is like to live in that part of the United States and any funding opportunities. Exchanging business cards or information is very common and the badge that you are given upon arriving even has a scanner square that the recruiters can use to keep in touch with you (they scan your badge and your e-mail is logged with them).

I spoke to over a dozen booths about their programs and had all my questions answered. I was even recruited during my poster session presentation! Which brings me to my next point.

  1. The presentations

The presentations are great for two reasons: 1. You have an opportunity to talk about your work and receive feedback on your presentation skills and 2. Other schools can come by your presentation and see you as a researcher. This is fantastic! I am not the best on paper in some ways, so having other schools approach me based on my science, reassures me that I am more than just my GPA or my GRE scores. Not only that, I received written evaluations based on my presentation skills and my poster, which were all constructive and positive!

  1. The seminars

The guest speakers focus on their journeys as minorities in the sciences and how their transforming experiences have brought them to where they are today. They inspire us to continue to pursue our passions and create a sense of community, which I will get to in a minute. The seminars are also great opportunities for junior scientists, like myself, because they offer an opportunity to check out new areas of research, hear about different paths in science outside of academia and get insights into how to be successful. There are workshops on how to give a compelling interview, what to expect in graduate school and how to master networking. All of these skills are important ones that give you a competitive edge.

  1. The experience

The experience itself was wonderful. Surrounded by 3,600 other students, mentors and researchers, the conference felt grand. I say grand because the conference center was massive, the sheer number of attendees was at times, a bit overwhelming, and the hotel that we were assigned to left me in awe. The Gaylord National Conference Center in Washington D.C. was an incredible place to hold this conference this year. As apart of the conference fees, we were fed in a large hall, which also created a sense of community.

  1. The sense of community

The SACNAS conference creates a sense of community for young scientists; a community that they can be a part of throughout their careers in the sciences. The idea of having a supportive community that I can be part of is a great feeling, especially coming from a background that does not have any college graduates. It can be lonely sometimes, walking into a completely new field that no one you grew up around, has any experience in. So, when I attended the conference with other San Francisco State students who were also presenting, they immediately considered me one of the group, even though we had just met. Similarly, other students from other places also welcomed conversation with open arms. The inclusion that occurs at SACNAS is excellent.

Overall, I highly recommend attending a SACNAS national conference. It looks great on your CV, it is great for your future scientific career and definitely gives you an edge when applying for graduate school. Bring your own business cards!

If you have any questions about SACNAS, please refer to the SACNAS website: http://sacnas.org .

Hope to see you there next year! I will be attending as a graduate student!

Feel free to contact me with questions at: blhansen “at” mail.sfsu.edu or missbridgette4 “at” aol.com. and indicate you read this blog so I know where the questions are coming from!

 

SACNAS

Shut up and write session in the CoDE lab

3 Mar

Today my graduate students held our first “Shut up and Write” session. Five students from my lab, two students from other labs and I participated. We met at 2 PM in the main room of the lab. Dwayne was in charge. At 2:05 he told us all to shut up and write. It worked! Everyone was silent. I cheated, because I had a bunch of reading to do, so I read, instead of writing, but I think that’s OK😉

At 2:25, Dwayne announced that it was time for a break. We all chatted a bit. I made a coffee for myself, a few people went to the bathroom. After 10 minutes, Dwayne told us to get back to writing and we did another 20 minutes of silent work. It was wonderful! Eighth people in the lab in complete (non-awkward) silence!

When we were done, I asked what everyone thought of the “Shut up and Write” session and it seemed that everyone agreed that it was surprisingly efficient. More work can fit into two times 20 minutes than we had thought. I was even thinking that for me it would be good to do this every day!