Thursday, May 23, 2019

PhD Defenses around the World: A PhD Defense from New Zealand

Today, I have the pleasure of hosting Shereen Asha Murugayah. Born and bred in Kuala Lumpur, Shereen recently completed her PhD "Engineering quorum-quenching enzymes" at the University of Otago. She is also a poet with work published in Shot Glass Journal, Rambutan Literary and the Poetry New Zealand Yearbook 2018. You can find her on Twitter @shereen_asha.

It is impossible to write about my PhD defence without acknowledging all the weeks surrounding it and the immense support I received from people around me. I was lucky that the bulk of my writing was during summer and at the end of the day, I could happily wander off into the warm buzz and bloom of the botanic gardens. While I wrote my thesis, my supervisor chose my thesis examiners: one from within my department, one within New Zealand and one outside of New Zealand. She read my drafts faithfully, always reminding me that what was important was how you told the story.

The five big milestones of the PhD submission at Otago as my lab mate Susie described were: submission for examination, the departmental seminar, oral defence, final submission and graduation.

The day I submitted my thesis for examination, my mum and lab mate Tom accompanied me. The graduate research school where all PhD theses are submitted was across the river from my department and for a few seconds, there was the wild thought of tossing it all in to the water. It must have been all the sun (heh). All students submitting their theses for examination receive a marshmallow fish. I don’t think I have ever had such mixed feelings about candy! I scheduled my departmental seminar before my defence so that I could practise my presentation. I had the privilege of having my mother attend my seminar and over the days after it, I got comments from people who came to my seminar saying they understood what I talked about. This was hugely gratifying as the department works on diverse research areas.

The oral defence isn’t really a one-day thing. It starts with receiving your examiners' reports, which I did within three months. This is average, but I have heard it can extend up to a year (!) depending on the examiners. The convenor of the PhD examination process thus has an important role in making sure things are progressing and are there to mediate conflicts if necessary. My biggest dread for my examination was that I would be asked to do more experiments. Considering my lab group was moving to Wellington, this would be complicated. To my immense relief, my examiners agreed that I could pass with minor revisions and the reports outlined the changes I needed to make. it pains me to say that my first thought after reading the reports was "Wow, I'm not actually a useless pile of crap". My second thought was a huge internal groan at the first thought.

The defence itself required a ten-minute summary followed by a page-by-page walkthrough of the thesis to address questions from the reports and any others that might crop up. I had two weeks to prepare. Understandably, I was nervous. I rushed through my summary and then we got down to the questions. The question I remember best was "What is the origin of quorum sensing?" That felt like a whole different PhD altogether! I speculated as best as I could. After the question session, my supervisor and I were asked to leave the room while the convenor and examiners deliberated. My lab mates waited with me while I lost my concept of time. Eventually, the convenor and examiners called me back and congratulated me on a thesis well-done! Tom had made a fabulous cake and my supervisor brought along some bottles of wine. My lab mates also wrote me a nice card and lovely presents. I walked home in cool sunshine, napped on my sofa then went out for celebratory drinks.

The two weeks after that were spent correcting the thesis and having it reviewed by my supervisor, departmental examiner and convenor. The examiners recommended changes that ultimately made my thesis better. The pressure was on to submit my PhD before my student visa expired. I had such a terrible cold the morning I went to have my thesis hardbound that my mother had to accompany me to make sure I made it there and back home safely. About a week later, I was ready for the final submission of my PhD “Engineering quorum-quenching enzymes”.

I do not know what the future holds for me. Both academic and non-academic paths are tricky and difficult. All I know is I will do my best.

Tuesday, May 21, 2019

Peer review preferences

A while ago, I ran a poll on Twitter in two parts about peer review preferences - I tried to identify the preference of authors and reviewers for peer review. It looks like traditional double blind peer review is the preference of the majority, with open review gaining popularity. In my field, single blind reviews are still the most popular method.

Here's the poll (in two parts) and its wake:

Thursday, May 16, 2019

Publication metrics

I recently ran a poll on Twitter on which platform is most used for publication metrics. While in my field it seems to be Scopus, the consensus of the poll is clear: Google Scholar!

Here's the wake of the poll

Tuesday, May 14, 2019

Papers and presentations from IALCCE 2018

Last fall, I attended IALCCE 2018 where together with my colleagues from TU Delft, I organized a Mini Symposium on Load Testing of New and Existing Structures.

For this MS, I submitted 4 papers as coauthor - 3 of these papers are the results of projects with B.Sc. thesis students from USFQ funded by my 2016 Chancellor Grant. During the MS, I presented my work on stop criteria and I also presented about diagnostic load testing of steel bridges on behalf of ADSTREN.

The abstracts of the papers are:
Proposed stop criteria for proof load testing of concrete bridges and verification
Eva Lantsoght, Cor van der Veen, Dick Hordijk
In a proof load test, a load representative of the factored live load is applied to the bridge. Since the applied load is large, stop criteria are important. Stop criteria for shear and flexure are proposed based on existing codes and guidelines, laboratory experiments, and theoretical considerations. This proposal is verified with the results from pilot proof load tests. The result of this comparison is that the stop criteria are never exceeded, or that they are exceeded only in the last load step. The proposed stop criteria are thus not overly conservative for application to field testing. However, information about the available margin of safety is not always available, especially for shear failures, and will need further experimental validation.

Nonlinear finite element analysis of beam experiments for stop criteria
Jose Eduardo Paredes, Eva Lantsoght
Proof load testing is used to assess the structural capacity of existing bridges. Stop criteria, based on measurements taken during proof load tests, determine if a test should be stopped before reaching the target proof load in order to maintain structural integrity. A nonlinear finite element model is proposed to investigate stop criteria. A reinforced concrete beam with plain reinforcement is modeled. The goal is to develop a reliable finite element model with adequate material constitutive models to analyze available stop criteria from existing codes. The beam experiment is verified in terms of strains. Stop criteria from ACI 437.2M-13 and the German guideline are analyzed for the beam model. The presented analysis shows that nonlinear finite element models can be used for the evaluation of stop criteria for proof load testing to limit the required number of laboratory tests.

Development of a stop criterion for load tests based on the critical shear displacement theory
Kevin Benitez, Eva Lantsoght, Yuguang Yang
The capacity of existing bridges is an important aspect regarding the safety of the traveling public.
Proof load testing can be a useful option to evaluate if an existing bridge satisfies the requirements from the code. The stop criteria provided by the Guidelines are generally suitable for flexure only. Therefore, in this paper, shear is considered. When developing a stop criterion for shear for proof load tests on existing bridges, many different approaches could be taken. Here, a stop criterion is developed based on the Critical Shear Displacement Theory. The development of the stop criterion is based on the analysis of the contribution of each of the mechanisms of shear transfer. The criterion is verified with experiments on beams in the laboratory. The consequence of this development is that now a stop criterion for shear with a theoretical basis is provided.


Verification of flexural stop criteria for proof load tests on concrete bridges based on beam experiments

Andres Rodriguez, Eva Lantsoght
When performing proof load tests, irreversible damage may occur. Guidelines for performing the test have been developed, which establish stop criteria to terminate the test before this happens. The stop criteria prescribed in the currently available codes are mainly designed for buildings, but load tests are also performed on bridges. This investigation compares the results from beams tested in the laboratory with stop criteria and analyzes their applicability on reinforced concrete bridges. The stop criteria from ACI 437.2M-13, the German guideline of the DAfStB, and a proposal developed by Werner Vos from TU Delft were evaluated. It was found that the DAfStB concrete strain stop criterion provided the most consistent results. The ACI stop criteria should only be applied if the ACI loading protocol is being followed. The deflection proposal by Vos, seems to be a reliable option, but further investigation needs to be done before it can be applied.

The slides of the presentations are:

Thursday, May 9, 2019

Introducing the Neuroethics Police Podcast

Today, I have the pleasure of hosting Katherine Bassil, the host of the Neuroethics Police podcast. Katherine is a neuroscience PhD candidate at Maastricht University in The Netherlands. She has gained interest in neuroethics throughout her studies and has attempted to integrate it in her work where possible. She hopes that one day she’ll be able to bridge the fields of neuroscience and neuroethics and hopefully inspire others to see the importance of such an effort. Follow her on Twitter @KatherineBassil and on Instagram @Katherine.Bassil

"It's time for the Neuroethics Police to make some arrests" is not a typical sentence you would expect to see "neuroethics" in. The Neuroethics Police? Not a common phrase, either. But I chose to build a podcast around this premise anyway. Why? To invite the curious, the skeptic, and the skeptic-turned-advocate to take part in the discussion of the ethics of neuroscience, a topic I believe does not have the attention it deserves.

My interest and curiosity for neuroethics, particularly the ethical and societal implications of neuroscience research, grew overnight after I attended a symposium on Neurolaw. After this symposium, I started thinking beyond the lab bench for the first time. It was shortly thereafter that I began my search for a neuroethics course within my masters' program in neuroscience to gain some more knowledge on the subject. I was met with disappointment; there was no sign of neuroethics at my university.

Why isn't there neuroethics training within our neuroscience program? Why aren't people (neuroscience students & professors, the public, etc.) aware of current neuroethical discussions? Why was I never aware of this -what I believed to be- important field before?

After graduating and moving onto my PhD studies, I was genuinely motivated to make this change, of bringing others' attention to neuroethics. I was determined to shine a spotlight on neuroethics and to show its importance. I was curious to learn the opinions of neuroscientists in my own department on current ethical discussions related to neuroscience. But I felt that individual discussions, however stimulating they may be, were not enough. I needed something broader, something more global, that could reach even those who had questions but didn't know where to begin. I had an idea - to start a podcast: The Neuroethics Police.

Why a podcast? I chose this format because I wanted to reach out to as many people as possible, and neuroethically-dense articles are, frankly, not everyone's cup of tea. Additionally, live conversations are unique and spontaneous, and there are many places a conversation can go which for a pre-planned format like a blog would never see. That's what I wanted for the audience of the Neuroethics Police, a platform that is accessible on the go, that is spontaneous, real and engaging all at the same time.

At the time I was starting this podcast, I was not sure if my goal to raise awareness on the ethical and societal implications of neuroscience research would come across as intended. But I learned a lot of important lessons after hosting just a few episodes.

1) Debate is a necessity

Since the first episode, I have been told that there is a need for more debate, more communication, and more discussion on the implications of neuroscience. Discussion is a necessity between scientists, ethicists, policy makers, government officials, and the public. There are no exceptions. One example reflected by the first guest of the podcast, Prof. Dr. Jos Prickaerts, is the need for guidelines concerning cognitive enhancement research. He particularly points out to how "tempting" certain research could be to some scientists and how the absence of strict guidelines may blur the lines between what is practically possible and what is ethically permissible. We need to get some of those pressing issues out there, to the public - including cognitive enhancement research, implications of neurotechnology, brain implants, to name a few - and not confined within the laboratory or university office walls.

2) Non-scientists have something to say

While preparing the list of potential guests to invite to the podcast, it was clear to me that my list was easily exhausted even when restricting it to neuroscientists and ethicists. But it didn't feel right to discuss societal implications of neuroscience research in the absence of members of society not immersed in academia. There are many informed decisions that concern society, and we tend to forget the public's voice in shaping these decisions. So, in the coming episodes, I urge all those interested, particularly non-neuroscientists to reach out and voice their opinion on topics ranging from neurotechnology and cognitive enhancement to biomarkers and other brain-related topics.

3) Ask the right questions

Developing thoughtful, fair, and non-biased questions remains the most challenging part for me in the process of creating an episode. Bias exists everywhere, even in formulating questions. I often found myself unintentionally imposing my opinion within the questions I ask. This has taught me to better identify bias and to more critically contemplate other people's work.

4) Voice your opinion

"I'm just a PhD student." That remark used to keep me quiet whenever I felt the urge to give my opinion during a discussion. But that's not necessarily a reason to keep quiet. The hierarchy in academia often puts students in a position to question whether they should speak up or not and whether their opinions are valuable. Bachelor, Master, or PhD students: we all have something interesting and important to say. In the coming episodes, I will be joining the discussion as well by challenging my guests' views, and so could you! The exceptional thing about the platform I use to create my episodes is that it allows the audience to interact with me or my guests by calling in during the recording session, asking questions or even commenting by sending a voice message that can be featured on following episodes.

My final message is this: there is a lot that needs to be discussed and the clock is ticking. For example, in the second episode, my guest and I discussed biomarkers for depression and aging and how their use could have potential ethical and societal implications. The implications we discussed include creating unnecessary anxiety in individuals who undergo similar screenings, but also the potentially discriminatory actions insurance companies might take in reaction to the development and application of biomarkers in clinics. The more people we have on board, the faster we can move towards more effective neurotechnologies, ethical neuroscience research, and an innovation-educated public.

Tuesday, May 7, 2019

Proof load testing of viaduct De Beek

I recently gave a presentation about a case study of a proof load test at the IABSE event organized by the national groups of Belgium and the Netherlands.

You can find the slides of the presentation here:


Thursday, May 2, 2019

PhD Talk for AcademicTransfer: The Challenges of Parenting and Academia

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 serious academic, you should spend all your waking hours working on your research and you should not have a life or family," some seem to argue, or that seems to be the undercurrent of some of the "I've had 4 hours of sleep over the last 6 days to finish the proposal" kind of stories you may hear some academics tell each other at conferences. Such a work rhythm is not sustainable - not for single academics, and not for academics with families.

With that said, being an academic parent can pose some challenges. As I'm learning more each day about what it means to be mom and an academic, and I'm interviewing fellow academic parents (which children in all age categories) about how they work as academic parents. While my conclusions about parenting is that every person does what works best for his/her family, I wanted to list a few challenges that are typical for academic parents and some ideas on how to overcome them.

1. Geographical isolation

If you moved away from "home" for an academic position, you may be geographically isolated from your family and friends - and not have anybody to rely on when you need an extra hand. Not being able to drop off your child for a few hours with the grandparents can be quite an inconvenience.

But wherever you are, you need a support network - it takes a village to raise a child, so you will need to build your village. If you don't have any family nor friends around, try to pair up with other parents who may be in the same situation (find them at your kid's or kids' activities). You can help each other out, and find moral support along the way. If you are having a hard time making friends with other parents, see if you can bring a grandparent to help you out for a few months (for example, when you return to work after parental leave). If none of these options are available for you, see if you can hire more help.

2. Low income

If you are/become a parent during your PhD years, you may be on a low budget. If your spouse traveled with your for your PhD and is not allowed to work because of visa restrictions, you may suddenly need to feed and house an entire family on a student stipend. While this is not impossible, and many students do so every year, you may find it challenging.

If you are on a low budget, see what your childcare options are for your budget, and if you possibly can get financial support for childcare from the government or your institution. If your spouse is not allowed to work, at least you save on childcare. To make ends meet, you may need to have a good look at your current expenses, and drastically cut down on certain categories. I've written about controlling your budget and ways to save money in the past - I personally think it's better to learn to live frugally for a few years, rather than to return home after graduate school with the burden of depth. Remember, this too shall pass.

3. Travel demands

If you need to travel to conferences or to a field site for research, parenting can become challenging. Travel is demanding for parents at many levels. When you are the mom of a nursing baby, traveling will mean that you need to accommodate pumping and perhaps send milk home. When you are a single parent, traveling overnight will require your child to stay with a trusted person overnight - which you may not have when you are geographically isolated. When your children are older, you will need someone to take care of all logistics at home when you travel.

There's no single solution to this challenge. Options include traveling with your child(ren) and a family member to see your him/her/them during the day, hiring more help for short periods of time, as well as cutting down on travel. I've significantly reduced travel over the last two years, and nothing bad has happened to me.

4. Irregular lab hours

If you need to run experiment on a certain time schedule, which may involve irregular hours, you will find that childcare can be difficult to arrange. Your partner may be able to jump in, but that's not always the case.

The key here is planning. If you know that a period of intense experimentation in the lab is coming up, start to look for your options in advance. Can you get extra hours in daycare? Do you have friends or family that can chip in? Can your partner trade hours at his/her job? Should you hire extra help? Should you delegate part of the experimental work to a student?

5. Inflexible tenure clock

Depending on the conditions of your tenure track, you may find that the tenure clock does not stop when you become a parent. If you work with chemical substances in the lab, it may be impossible to continue experiments during pregnancy. You may fall behind the tenure clock during maternity leave, and then you may decide to work part-time instead of full-time, but the tenure clock won-t adjust to your new schedule.

If you are faced with an inflexible tenure clock, speak up about it. It's not a fair system, and it should be changed so that parents don't get cast to the side because of the tenure clock. Ask for your options. Insist where you can - this battle is worth a fight, as it will improve the conditions for the generations that come after us.

6. Working environment

If you are constantly hearing other people brag about all the hours they put in to their academic work, you may feel out of place. If you are the only parent in a research group, you may feel that your colleagues don't understand your struggles.

To make academia more sustainable, we need the working environment to change and to be able to accommodate people with different backgrounds and with different situations at home. To solve the world's pressing problems, it's all hands on deck - we can't afford to lose good researchers simply because the working environment is hostile towards parents. If you feel that your colleagues don't understand your struggles, build your own network of academic parents to help each other out and to share your best advice.
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