Thursday, October 27, 2016

Drink less coffee during your PhD

Today's guest post is a contribution from Seán Mac Fhearraigh, PhD. Seán was a PhD student at University College Dublin & a post-doc a Cambridge University where he studied mechanisms of cell division. Currently Seán run’s an ELISA assay company where you can find some great information on ELISA assay protocols and ELISA kits.

Caffeine or 1,3,7-trimethyl-1H-purine-2,6(3H,7H)-dione 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione (as it is chemically known according to IUPAC) is the fuel that runs the scientific community: it helps many scientists get through late nights in the lab, provides them some extra focus when they are fatigued and provides a common meeting point for Professors, Grad Students and Post-Docs to complain about life in the lab. Not even the lab rats are safe with nearly 5,000 publications found under "Rat AND Caffeine" in PubMed.Gov.

Not all of us, but most of us, become addicted to caffeine at some stage during grad school or our post-doc, if not worryingly earlier in our lives. You just have to attend a conference to see the addiction to caffeine is rife throughout the scientific community. Coffee before morning lectures, coffee during the morning break and lunch, and then some more coffee in the afternoon session break. Last year during the American Association for Cancer research, a biotech company that provided free coffee was one of the main attractions at the conference with up to 50 people waiting in line to get their free coffee constantly throughout the day.

Coffee does have some great benefits and has been shown to increase endurance during athletics and increase focus following tiredness. However, not everyone drinks the prescribed doses of coffee everyday, with many drinkers consuming a few cups to keep them alert so they can get through the daily slog counteracting some of the benefits associated with coffee consumption.

During my PhD, I became dependent on coffee: without my caffeine kick in the morning at about 10:30 am I found it impossible to get through the day. Getting that first coffee in the morning was consuming and prevented me from starting many experiments and made me make half-hearted attempts to start assays in the morning. The mention of coffee by a lab mate would instantly make me drop what I was doing and run downstairs to the coffee shop and order a double shot Americano. There was no experiment that I would not stop, delay or bin just to get that coffee and potentially a muffin. They had a great deal on of coffee and a muffin for 3.50 pounds so how could I resist! Caffeine, sugar and fat was to power me through the rest of my experiments for the day. Following my strong coffee I would get a rush of adrenaline, feel more anxious and stressed, and look for options around me not to do lab or desk work. Ironically, I was looking for caffeine to give me a boost or energy to perform my experiments, but instead it made me sometimes lose focus, become jittery and anxious. According to the NIH caffeine too much caffeine can result in: restlessness, anxiety, and irritability. It may also keep you from sleeping well and cause headaches, abnormal heart rhythms, or other problems.

And that was just morning... By the time 3'o clock arrived, I would be on the slow and painful caffeine slump, assays were now harder to set up, papers were harder to read and my stress levels were through the roof from not getting my experiments done because I went for coffee that morning. So what better way to combat the slump but go and get another coffee. Having another coffee would allow me to work a few more hours, or even into the night where I could catch up on where I missed out during the day. However, this time I would be more hyped up on caffeine and looking for any other distraction so I wouldn't have to do some lab work.

Like weaning yourself off heroin, the withdrawal symptoms from caffeine can be headaches, anxiety, vomiting, sleepiness, muscle pain, depression and lack of concentration. However, if this meant that you would be less anxious, more focused on lab work and didn't fear the small problems in the lab it would be worth it in the long run.

Looking back on my PhD and Post-Doc I definitely think I could have shaved a good few months off my 5 year PhD if I didn't drink coffee and would have been more productive during my Post-Doc instead of running off for every little break to have a coffee. And who knows, I might have got that Nature paper!

Tuesday, October 25, 2016

How to switch to a plant-based diet

My mom's main advice throughout exams and periods of hard workd was always: make sure you eat well and sleep enough. I've written about sleeping enough in the past, and I've mentioned you should eat well and not live on vending machine snacks if you want to stay healthy and productive.

Before I continue, I want to share a word of caution with you, or actually two words of caution - if you allow me. The first one is that I am not a nutrionist. If you are planning to make drastic choices with regard to your food, it can be wise to consult a doctor, and/or track your (micro)nutrient intake to make sure you get everything you need. You can do this tracking for example through my fitness pal. Second word of caution: I'm not writing this post to "convert" anybody. If you want to include more plant foods in your meals, this post is for you. If you want to go fully plant-based, I'm happy for the animals, the environment, and you. If the idea of eating vegetables creeps you out, then do please track your food intake to see if you're not missing any vitamins.

For many of us, eating healthy will mean including more fruit and vegetables into our meals, which are chockful of micronutrients. If you switch from salty, fatty take-out food to bowls of grains, vegetables, and a source of protein, you might already start to feel a difference in your energy levels. In today's post, I will focus on how to switch to plant-based meals. You might like to try and have a veggie meal once a week to see how it works for you. Or you can use some of these ideas to prepare more vegetables, and then have a piece of animal protein on the side.

With that said, let's have a look at how you can switch to a diet that is richer in plant foods, if you want to up your intake of fruit, whole grains, legumes and vegetables. Here are some tips you can use to make this transition:

1. Replace animal protein with a bean dish or a plantmeat

If you grew up eating meals of potatoes, meat, and vegetables, it is actually not very hard to switch the meat for a bean dish or a plantmeat. If you're not used to eat beans/legumes, make sure you buy them dried, soak them for 24 hours, wash them very well, and then cook them - nd give your body some time to get used to digesting beans. There are a large number of commercial "plantmeats" that make replacing animal protein even easier: every supermarket sells a veggieburger that you can use. Just keep in mind that these processed plantmeats are still a processed product, sometimes high in sodium, and that antyhing you whip up from scratch in your kitchen is usually healthier, and certainly fresher.

2. Dairy is easy to replace

Milk is for calves. If you need dairy in a recipe, you can easily replace it with a plantbased equivalent. You can make your own nutmilks if you have a blender and a fine meshed bag, or you can buy it from the grocery store (just make sure the first ingredient is not sugar). If you are used to cook with a lot of cream-based sauces, explore other possibilities, and switch to vegetable-based sauces. A simple example is to replace alfredo sauce by arrabiata sauce.

3. Baking without eggs is not hard either

There are plenty of conversion charts you can find on the internet, such as this one below:

Flaxseed with water works wonders for binding dough, a bit of extra baking powder goes a long way in cakes, and mashed banana or applesauce thicken and sweeten dough. I'm especially a fan of getting some flaxseed into my desserts, given the micronutrients flaxseed has. (All those B-vitamins!)

4. Discover all the available whole grains and root vegetables

There is more to carbs than pasta, bread, potatoes and rice. Switch up your palate by trying out other whole grains, such as quinoa, amaranth, buckwheat/kasha, and all the other grains you can find. You can simply boil them, use them as flour in breads or desserts (pancakes with wheat and buckwheat flour are the best), or even buy products derived from them (there's pasta based on everything out there).

Similarly, you can switch up your regular potatoes and discover sweet potatoes, yuca, yams or plantains - one of the fun parts of going plant-based is that it is an invitation to trying out all the plantfoods out there, and break out of your regular food patterns.

5. Salads don't need to be boring

If you think a salad is just lettuce, tomato and cucumber, you might need to think again. There's just so much that you can add to salads. For flavor, try olives, artichokes, sweet corn, toasted almonds, or jalapenos. For protein, try chickpeas, black beans, lupine seeds, pieces of tofu or seitan, or lentils. For texture, add grilled vegetables or croutons or toasted dried corn. Add a vinaigrette (oil, lemon juice, a bit of mustard, and any variation of herbs or juice) to season everything and enjoy.

6. Try out veggie restaurants and recipes

To remain inspired, try out veggie restaurants and recipes you find online. You might taste something you hadn't thought of before in a restaurant, and then try to recreate the plate at home. If you're stuck in a rut, you can always look for some recipes with high ratings online and try these out.

7. Find some standard meals that work well for you

Sometimes having a bit of a rut is not a bad thing. If you have a few standard meals that work well for you, then you can lean back on these options if you are pressed for time or without inspiration for trying out something new.

Some standard options for breakfast are: pancakes, bread with avocadomash, smoothie (possibly with a plantbased protein powder)
For lunch: big salad, a sandwhich with smoked tofu, a bowl of grains-vegetables-beans, a big cup of vegetable soup
For dinner: pasta with tomato sauce and grilled mushrooms, potatoes with sauerkraut and veggie sausages, vegan pad thai, veggie-based pot pie, rice with chili, ...

8. Meal prep

If you want to make sure you have your healthy foods on hand, then prepare them. Cook in big batches, and freeze some parts for later. Cook one evening a week two or three dishes for your dinner for the rest of the week, if you don't have time every day to cook a fresh meal.

9. Talk about it

Tell your friends and family that you are trying out a plantbased diet. Explain them why you are doing this (the environment? the animals? you want to try out and see if it makes you feel more energetic?), and I'm sure they will understand. Bring some of your food so they can try it out and learn that plantbased food is not bland.

10. Know where and when to shop

You can say that vegetables are quite expensive, and that plantbased foods are too expensive to rely on. If you cook in bulk, you can buy vegetables in large quantities at a farmer's market. Grains and legumes in dried bulk are cheap as well. The expensive foods are actually the processed plantmeats, and those you can keep for a special occasion every now and then. Some supermarkets give discounts on fruit and vegetables a certain day of the week (the Megamaxi chain in Ecuador gives 20% off fruit and vegetables on Wednesday, for example). All little savings can help you be plantbased on a budget.

Thursday, October 20, 2016

Q&A: Working from your parents' house

I recently got an interesting question, of which I'd like to share my answer with you.

Here´s the question:


This is a random cry for help but I am writing my dissertation and just moved back in with my parents at the same time. Uninterrupted writing time is impossible, I am now the maid and house project do-er of all things and I haven't written a word. My defense is in October and I'm teaching part time at a local university. I have my dual monitor set up and all my resources here at the house so working elsewhere hasn't really worked well for me. Any advice on navigating this without being a terrible person and telling my parents to leave me alone!? I'm also almost 30 and have been out of the nest for over 10 years just moved back in to save money. I feel so ungrateful but I can't get anything done and I need to graduate! Thank you so much...

This is what I answered:

Hi Reader,

Thanks for reaching out to me through my blog.

I understand you are in quite a complicated situation, and that it might be hard to work from your parent's house. Way back when I was still studying in Brussels, I returned homw to study for exams while my parents had health problems, and it was difficult balancing studying and taking care of them (and worrying). After my PhD, I returned to my parents' house while I prepared for my move to Ecuador, and tried to work over distance for TU Delft. My mom was very happy to have me back with her, so it was hard for me to shove her off and tell her that I really needed to concentrate on writing that paper... Long story short, I understand how being back at your parents house can not be an ideal situation, and how you also try not to come across as grumpy and ungrateful.

With that said, I think there are a few things that can help you:

1. Make a to do list
If you need to fix things in the house, cook, run part of the household and all that, it helps to make a todo list. You can't fix all the problems of the house in a day or in a week, so you might want to make a list of what you want to/need to do first, and then distribute that over time.

2. Make a planning and a schedule
Distributing tasks over time, you might for example think of what you can reasonably do in 1 - 2 hours a day. Clean the bathroom, cook, and replace the shower curtain, for example on one day; groceries, making soup, and giving the kitchen a good cleaning the next day? You can, for example, block the time period 5pm - 7 pm for those tasks. You can use google calendar to make a weekly template. Put in your calendar your teaching hours, including the commute, and then see if you can reasonably fit, for excample, 10 blocks of 1,5 to 2 hours in your schedule for writing, so that you know that those need to be your uninterrupted writing times.

3. Pomodoro?

Have you tried the pomodoro technique of working in short bursts of time? You can set a timer for 20 minutes to draw a specific figure, write a certain paragraph, revise a literature source. After 1 pomodoro, you get 5 minutes of break, psosibly to interact with your parents - you can come out of your room and have a quick chat with them. After 4 pomodoros, you take a 30 minute break - have a coffee with your parents and talk a bit with them.

4. Noise-canceling headphones
I love noise-canceling headphones. They are big and chunky, help to obliterate all the noise from outside, and they also signal to other people "I'm busy, please come back later". They are rather pricey at about 300 euros, but if you can spare the money, it's a really good investment.

Do these ideas help you? Please let me know how it is going.


Tuesday, October 18, 2016

Probabilistic prediction of the failure mode of the Ruytenschildt Bridge

We recently published a paper about the probabilistic analysis of the failure mode of the Ruytenschildt Bridge in Engineering Structures. You can download the paper for free for a month before it goes in hiding behind a paywall.

The abstract is as follows:

In the Netherlands, the shear capacity of a large number of existing reinforced concrete solid slab bridges is subject to discussion, as initial assessments indicated that their capacity was insufficient. In certain cases, the deterministic value of the moment capacity is larger than the deterministic value of the shear capacity. However, when the variability of the material properties, and of the capacity models themselves are factored in, a probability of a certain failure mode can be calculated. Here, a method is introduced to calculate the chance that a cross-section fails in shear before it fails in bending.

The method that is derived here is applied to the Ruytenschildt Bridge. This case study is a reinforced concrete solid slab bridges that was tested to failure in two spans during the summer of 2014. The relative probability of failure in shear of the bridge was determined. The predictions indicated a smaller probability of a shear failure than of a bending moment failure. In the first tested span, failure was not reached, but indications of flexural distress were observed. In the second span, a flexural failure was achieved, in line with the probabilistic predictions. The presented method can be used in the assessment of existing bridges to determine which failure mode is most probable, taking into account the variability of materials and capacity models.

Thursday, October 13, 2016

I am Lana Sinapayen, and This is How I Work

Today, I am inviting Lana Sinapayen in the "How I Work" series. Lana was born near Paris but raised in Martinique, a small French island in the Caribbean. She stayed stayed in Martinique until the end of high school, then joined an engineering school in Lyon. During her engineering years, she had the chance to travel to China, Vietnam and Japan. She liked Japan the most and went back several times before finally moving there in 2012.

Current Job:
PhD Student
Current Location: Department of Complex Systems, Tokyo University, Japan
Current mobile device: Android

Can you briefly explain your current situation and research to us?

I am in my 2nd year of PhD at the Ikegami Lab and I specialise in Artificial Life / Artificial Intelligence.

I was born near Paris, but raised in a small French island in the West Indies (Martinique) where I lived until I graduated from high school. I then went back to the continent to attend an engineering school where I had the chance to learn new languages, like Japanese, and do an internship in the country. I decided to move to Japan before completing my Engineering degree and obtained an agreement that allowed me to get both a French degree as an IT engineer and a Japanese Master's degree in Mathematics and Information Sciences from Tohoku University. In the meantime I worked for several Japanese companies as an intern.

After getting my Master's I moved from Tohoku to Tokyo for my PhD. I now share my time between my research and a part time job to fund my education.

What tools, apps and software are essential to your workflow?
I spend much of my time presenting my research in conferences, at the lab or in papers, so my most essential tools are presentation tools. I use Google Drawings to sketch diagrams, R Studio to make figures from numerical results, and Prezi to shape up oral presentations.
I am a programmer at heart, so for my research itself I make my own tools and softwares.

Twitter is a wonderful tool to keep up with the latest interesting papers being published in fields that are close to mine but that I do not follow with assiduity.

What does your workspace setup look like?
As long as I have a computer, I can work anywhere. I work mostly at the lab, which has 3 rooms. I like to use the smallest one when I really need to concentrate; the biggest one when I want to discuss with my labmates. I also sometimes work at the library, in coffee shops before going to my student job, or simply at home.

What is your best advice for productive academic work?

Take a step back. It is easy to get very absorbed by a project, especially when deadlines approach. I have my best ideas when I let my mind wander: while riding the bus, eating lunch or listening to someone else's ideas. When I try to be single minded and concentrate too much on a project, I loose creativity. I end up putting a lot of time and effort into things when, in retrospect, it would have been much more productive to step back and think.

How do you keep an overview of projects and tasks?
I usually don't need to: the constant stream of emails and face-to-face discussions is sufficient to remind me of milestones and deadlines. I am lucky enough to have freedom in how I set my schedule. When I am really anxious about particular events, I use Google Calendar.

Besides phone and computer, do you use other technological tools in work and daily life?
Not really, except when working on particular projects. For several months I wore a mini-camera that essentially recorded my day in pictures, but this project is now finished. I use my phone a lot, especially because I like to build applications that are tailored to my needs.

Which skill makes you stand out as an academic?
I am not afraid to ask questions, express my ideas or admit my ignorance to other researchers and discuss theoretical concepts. There is absolutely no gender balance in my field, I am still a student, and I am sometimes the only foreigner in the conference room, so it could be easy to feel intimidated and refrain from discussing interesting or polemic points with other researchers.

But you do not get over these specifics without having a curious, assertive personality. I love reading scientific books or papers; discussing and criticizing them makes me feel enriched with new ideas and knowledge.

What do you listen to when you work?
Nothing, except if the place is noisy. Then I just let YouTube play random songs to mask the noise.

What are you currently reading? How do you find time for reading?

I read science books, science fiction books, or just fiction. But mostly I read scientific papers and the news. Since I have started working part time, I have unfortunately lost the time to read real books, or only just a few pages at a time.

Are you more of an introvert or extrovert?
I am an extrovert with my friends, I talk a lot and ask many questions, but I need a great amount of "alone time". An hour of interaction is usually enough to drain me, and I will need quiet time to recover. I am also really bad at interacting with several persons simultaneously. I can only focus on one or two people at a time.

What's your sleep routine like?
I normally sleep 7 to 8 hours, although I enjoy sleeping obscene amounts of time when I can afford it... When I am busy I sleep 4 or 5 hours per night, but I am not myself when I am tired.

What's your work routine like?
I don't really have a routine. I am always working on different things, there are always different events to attend to, and both my lab and my part time job have free hours. Not two days are the same, so I work as soon as I get some free time.

Tuesday, October 11, 2016

Ruytenschildt Bridge: Field and laboratory testing

We recently published a paper on the field and laboratory testing of the Ruytenschildt Bridge. This bridge was tested to failure in two spans, and then beams sawn from the bridge were tested in the lab to study the behavior further.

The abstract of the paper is as follows:

A large number of existing reinforced concrete solid slab bridges in the Netherlands are found to be insufficient for shear upon assessment. However, research has shown additional sources of capacity in slab bridges, increasing their total capacity. Previous testing was limited to half-scale slab specimens cast in the laboratory. To study the full structural behavior of slab bridges, testing to failure of a bridge is necessary. In August 2014, a bridge was tested to failure in two spans. Afterwards, beams were sawn out of the bridge for experimental work in the laboratory and further study. Though calculations with current design provisions showed that the bridge could fail in shear, the field test showed failure in flexure before shear. The experiments on the beams study the transition from flexural to shear failure and the influence of the type of reinforcement on the capacity. The experimental results were compared to predictions of
the capacity for the bridge slab and the sawn beams. These comparisons show that the current methods for rating of existing reinforced concrete slab bridges, leading to a sharper assessment, are conservative. It was also found that the application of plain bars instead of deformed bars does not increase the shear
capacity of beams.

You can download the paper for free until November 12th 2016 via this link.

Thursday, October 6, 2016

PhD Talk for AcademicTransfer: Surviving and thriving in academia as a young female academic

This post is part of the series PhD Talk for AcademicTransfer: posts written for the Dutch academic career network AcademicTransfer, your go-to resource for all research positions in the Netherlands.

These posts are sponsored by AcademicTransfer, and tailored to those of you interested in pursuing a research position in the Netherlands.

If these posts raise your interest in working as a researcher in the Netherlands, even better - and feel free to fire away any questions you might have on this topic!

As a young female academic in a male-dominated field, I sometimes stick out like a sore thumb. My goal for today is not to convince you that there is such a things as gender bias in academia. Sufficient research has proven this. An overview of all studies is here, with some recent publications here, and here , and let's not forget that, once a female academic is hired, students will give her lower ratings as well.

With that said, I don't want to discourage any young aspiring female academic. Please no, academia needs all talent on board. But you'll need to brace yourself and learn to let them haters be haters. Story of my life - and the fact that combined studies with music confused people around me even more. Like a "typical" female academic, I've had my doubts and imposter trouble. But growing into an independent scholar, in my little niche of research, has helped me put things in the right perspective. And even though I don't have a storybook resume(who goes to potter around somewhere in the Andean mountains, isolated from the rest of the research community in concrete bridges anyway?), I am content with my progress, and I'd like to believe my research is adding value to society.

So how did I come this far? How did I do my own Dr. Strangelove and learned to stop worrying about rejected papers, missed opportunities, and collaborations in which I am not involved, and love the bomb (whatever it is)? Even though I am still an early career researcher, I think there are a few pieces of advice I can give you.

1. Don't feed the trolls

At every stage of our career, there will be trolls and haters and naysayers. You'll be watched more closely than your male colleagues, and for random things like your clothing and hair and whatnot. And while I'm the last person to say I've never been offended or shocked or outraged by certain comments, I have also learned that worrying and getting angry is not going to get you anywhere. Acknowledge that it is a hater's comment, accept how you feel about it, and then move on and prove them wrong.

2. Build a community and network

Women are bad at networking, "they" say. While I generally think that dividing humans in "women do this" and "men do that" is overrated anyway, I think there are simply different networking styles. As an introvert, I'm not the type of person to barge into people and wave my business card in front of their nose. But I do genuinely care about the work of other people, and I enjoy a good research discussion like any other good ole nerd. I frankly don't think you need to suit up and shake hands all the time to build a community. You can have one-on-one conversations with other researchers at conferences (just ask someone who looks a bit lost what brought him/her to the conference and what he/she is working on). You can use online tools to reach out to other researchers and share information. There are plenty of ways to get in touch with fellow scholars.

3. Find ways to reach out

In line with my previous recommendation, find ways that work for you to reach out to fellow scholars, the industry and/or the broader public. How about starting a blog about your research? Or contact the organizer of podcasts to talk about your work? Or write a guest post for an existing blog, if the idea of maintaining a blog by yourself seems to be a bit too time-consuming (I love hosting guest writers)? In which medium does your voice resonate? Find your voice, and don't be afraid of letting it sound.

4. Volunteer

Along with different styles of building community come different styles of contributing. I tend to be quiet in meetings, and speak few sentences if I have an opinion that needs to be voiced. But I contribute in my way, by volunteering when work needs to be done. Yes, your research and papers are important, and need a lot of your time, but showing up and doing work in different communities (university committees, technical committees, organizing events for your research group) will help you develop skills you will need in your future career. Don't be shy and raise your hand.

5. Don't drop the ball

Disclaimer: I don't want to worsen anybody's perfectionism here. But: don't drop the ball on work you take on. If you raise your hand, make sure you can deliver on time. Because then the haters will come and double hate. So while this advice might sound as if you have to work double as hard to show that you are a legit researcher, I think a lot comes down to managing your time and making smart choices and generally kicking arse.

6. Critique your own biases

When you think a female researcher comes along as uncertain, immature, poorly dressed or whatever thought might pop into your head, acknowledge your cultural conditioning. And then send it to Pluto. The times won't change if women themselves get stuck in thinking less about other women.

7. Pay it forward

And until the times will have changed, you can pay it forward and help the careers of fellow female researchers. If you're asked to suggest reviewers, see if you can bring some diversity in your nominations. If you see a female student doubting her abilities, talk to her. If you see a female graduate student doubting about whether or not she is PhD material, address her concerns. In the end, our research communities will function better if we can get all talent aboard, and if nobody falls off the wagon for not being the right gender (or race for that matter).