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PhD journeys at Great Ormond Street Institute of Child Health

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Going rogue on the Bogue: my Bogue Fellowship at SickKids Hospital, Toronto

melanie.koelbel.157 November 2019

Written by Daniyal Jafree a MB/PhD student, supervised by Dr David Long and Professor Peter Scambler in the Developmental Biology and Cancer programme, studying how lymphatics in the kidney develop. Lymphatics are specialised tubes which clear debris, excess fluid and immune cells from organs. They have important roles in kidney disease, but how they appear and grow in the kidney in the first place has been a complete mystery.

The first year of my PhD was spent characterising how lymphatics normally grow in the kidney. Based on experiments I did, we had a strange idea about precisely where the cells that make lymphatics in the kidney might be coming from. However, we faced a major roadblock, as we didn’t have access to the right techniques to test our strange idea. Actually, no one in the UK did. With 2-3 years of my PhD left, a unique problem to solve and no way to solve it, what am I to do?

A few Skype calls, a short application form to UCL’s Bogue Fellowship scheme (https://www.ucl.ac.uk/prospective-students/scholarships/graduate/UK-EU_Res/bogue-fellowship) and a 7-hour flight featuring two screaming babies later, I found myself at the Peter Gilgan Centre for Research and Learning (PGCRL) at SickKids Hospital, Toronto. PGCRL is the equivalent of GOSICH in Canada, and SickKids is the largest centre dedicated to improving children’s health in the country. After acclimatising to Toronto’s skyscrapers (my apartment was on the 37thfloor), the team of Professor Norman Rosenblum (my supervisor in Canada) and I tried to tackle the mysteries of kidney lymphatic development using gene editing strategies to trace stem cells in mice.

Thanks to tremendous luck, an extremely supportive team and a mouth-wateringly fancy microscopy facility at PGCRL, it took us 9 weeks to test our strange idea of where lymphatic cells in the kidney are coming from. What we found was really surprising, and challenges what we thought we know about how lymphatics develop. The next trick will be to test whether we can exploit this to target lymphatics in kidney diseases; an ongoing aim in David’s laboratory.

I’m grateful to David for facilitating the trip, the GOSICH team and the MB/PhD programme for allowing me to go and Norm in Toronto for getting me involved in the amazing environment at SickKids. Whilst out there, I even got some time to travel, visit family and explore the Canadian wilderness.

Bottom line – if you’re a PhD student with an interesting idea and some time left till your thesis is due: go rogue. Go Bogue.

UCL Grand Challenge (2018- 2019): What are you looking for? Development of a novel spatial memory test for children.

melanie.koelbel.1516 October 2019

Written by Melanie Kölbel, 3rd year PhD student at the Great Ormond Street Institute of Child Health (GOSICH), researching sleep in sickle cell anaemia and Mina Jeon, 3rd year PhD student in the department of Psychology and Human Development at the Institute of Education (IoE), researching sleep and cognition in neurotypical and autistic children. Both are part of the Lifespan Learning and Sleep Laboratory (LILAS) at UCL.

Logo of the Visual Spatial Memory Task for children (VISMO-C) at the ages of 5 – 16 years old.

 

Tweet:

UCL Grand Challenges: @UCL_GC

Lifespan Learning and Sleep Laboratory (LILAS): @LILAS_Lab

Mina Jeon:@MinaJeon12 


Think about the following. How many times have you asked yourself or your child(ren)?

  • “Where is my/your […] ?“ (<- insert any objects that you or your child(ren) misplace frequently in the brackets).
  • “I know I put […] here?” or “Don’t you remember where you put […] ?”(<- insert any objects that you misplace frequently in the brackets).
  • “Am I lost again?” I could swear it was that way.

How does a better spatial memory help children? Certainly, it helps them to be successful in STEM.

In the early years, motor development enables a child to explore the world around them. Exploration of the new world helps the child to develop the relationship between objects and places and, therefore, the maturation of spatial cognition (Postma & Ham, 2016). Already at the age of 3-months, young children show an understanding of object misplacement (Hayne et al., 1991). At 4-years of age, children are able to use landmarks as clues to find their way around (Waismeyer & Jacobs, 2013). Spatial cognition has been shown to play an important role in the development of creativity and aids successful expertise development in the domains of STEM (science, technology, engineering, and mathematics) (Kell et al., 2013; Lubinski, 2010; Wai, Lubinski & Benbow, 2009). Unfortunately, it is often neglected in educational assessments (Kell & Lubinski, 2013).

Have you seen my dots?

Have you or your child looked for dots recently? One of the tests available to assess spatial memory in children is the Dot Locations Test in the Children’s Memory Scale (CMS) (Cohen, 1997). The child has to remember the locations of either 6 or 8 dots over three trials. After a learning stage, the dots need to be recalled on two occasions: (1) immediate after a distractor was shown and (2) after a long delay (20 ~ 30 minutes) to assess the child’s visual spatial memory abilities. The test appears to have a low ecological validity, since it is less generalizable to a real-life setting. From our current experience the test does not seem to be as useful for typical developing children as for children who have an obvious visual or spatial memory difficulties and therefore might underestimate a child’s true performance, especially during the early years.

Pictorial representation of the Dots Location Task for children at the ages of 5-8 years (6 dots) and 9 – 16 years (8 dots) in the Children’s Memory Scale (CMS).

 

Why not develop a new spatial memory task that is more ecologically valid?

We applied for the UCL Grand Challenges Doctoral Students Small Grants Scheme to receive funding to create a fun, ecologically valid and easy to administer test for children to assess their spatial memory. We decided to create a booklet that shows two scenes of an organised and disorganised bedroom with different objects in it. The test follows the Dot Locations principle, whereby the child has to remember the locations of 7 target objects over three trials. After a learning phase, the objects need to be recalled on two occasions: (1) immediate after a distractor was shown and (2) after a long delay (20 ~ 30 minutes). The reason behind our choice of organised and disorganised bedroom scenes is that the bedroom is a place where children keep their belongings/possessions and are generally most familiar with. The organisation of the bedroom could give us a better understanding on how objects are best remembered depending on the environment they are in. The CMS lacks this kind of information. An important implication of the newly developed visual spatial memory test is that by knowing how a child can remember things in either an organised and/or disorganised way, it can help us to create targeted future interventions.

(1) Top left: VISMO-C with Manual, stimulus, record form and consent form; (2) Top right: Mina and myself after receiving the first copy of the test; (3) Down left: A child taking part in the assessment and (4) Down right: VISMO-C organised bedroom scene.

 

Challenge accepted: The challenge within the challenge. 

The first challenge we encountered was the design of the test. We had the idea and framework drafted, but we had no artistic knowledge and skills. Having the ability to draw like a 5-year-old clearly does not help. Certainly, it is great to have lots of ideas, but if you are missing the skills to bring these to life, it really puts a break on your work. We didn’t have time to spend hours learning the methods to design the room professionally. Luckily, a great friend and colleague, who is working as a freelancer in design, was able to help us out.

Once this was sorted, we faced the challenge of recruitment. We made flyers, which we handed out on high streets, parks and shopping centres, we even contacted schools, but responses were low. Often kids would be excited if we approached families and were willing to take part, but parents were more reluctant and never got in contact with us. What really helped in the end was the willingness of colleagues and families we work with to spread the word and to engage their friends in this research. Part of the research also assesses their children’s sleep and general cognitive abilities and parents were interested in finding this out too.

Recruitment flyer for the study.

The challenge that still persists is the assessment of a child’s spatial memory skill in a real-life setting. It was our goal to take children to the British Museum for an hour and to walk a maze with them to find out if they can retrieve the way to get to the targeted masterpieces. However, parents often could not find the time to come in. Unexpected closures of our planned routes within the museum and crowdedness made it impossible to fulfil this part of the challenge. In psychology, history taking is very important and can aid the understanding of underlying problems (Postma & Ham, 2016). Therefore, we aim to ask parents specific questions regarding their understanding of their child’s daily spatial memory performance. Working together on this project has shown us that one should not be afraid to ask, and that teamwork can combine multiple skills and make something incomplete complete. We are excited to start analysing the data soon and hope that the VISMO-C will be a useful measurement to test a child’s spatial memory performances in the future, especially in the early years.

The recruitment is still ongoing and your child will receive a £10 voucher for participation.

Please get in contact with Mina Jeon (mina.jeon.12@ucl.ac.uk) and Melanie Kölbel (melanie.koelbel.15@ucl.ac.uk).


Acknowledgement:

  • UCL and the UCL Grand Challenge Scheme for providing us with the funding to make the project possible.
  • Special thanks to the continuous support of our supervisors Professor Fenella Kirham and Dr. Dagmara Dimitriou
  • Katja Dallmann for helping us designing the rooms and objects for VISMO-C.
  • Celia Brenchley, for her advice and valued experience in educational psychology.
  • Special thanks to all the families and children who have played the game with us.
References:
Cohen, M. J. (1997). Children’s memory scale. Administration manual. San Antonio, Texas: The Psychological Corporation.
Hayne, H., Rovee-Collier, C., & Borza, M. A. (1991). Infant memory for place information. Memory & Cognition, 19(4), 378–386.
Kell, H. J., Lubinski, D., Benbow, C. P., & Steiger, J. H. (2013). Creativity and technical innovation: Spatial ability’s unique role. Psychological science, 24(9), 1831-1836.
Kell, H. and Lubinski, D. (2013). Spatial Ability: A Neglected Talent in Educational and Occupational Settings. Roeper Review, 35(4), pp.219-230.
Lubinski, D. (2010). Spatial ability and STEM: A sleeping giant for talent identification and development. Personality and Individual Differences, 49(4), pp.344-351.
Postma, A. and Ham, I. (2016). Neuropsychology of Space Spatial Functions of the Human Brain. Amsterdam: Academic Press, pp.309-352.
Wai, J., Lubinski, D. and Benbow, C. (2009). Spatial ability for STEM domains: Aligning over 50 years of cumulative psychological knowledge solidifies its importance. Journal of Educational Psychology, 101(4), pp.817-835.
Waismeyer, A. S., & Jacobs, L. F. (2013). The emergence of flexible spatial strategies in young children. Developmental Psychology, 49(2), 232–242.

PhD: a road to success but make sure you stop for fun along the way!

Emma J Butcher8 April 2019

Authored by Melanie Kölbel, a 2nd year PhD student at the Great Ormond Street Institute of Child Health (GOSICH) researching sleep and sickle cell anaemia. Loves outdoor activities and travel. Lead organiser for the GOSICH Postgraduate Society.

Tweet the GOSICH Postgraduate Society at: @ICH_PGsociety

 What does PhD REALLY stand for and why should you (the GOSICH PhD students) follow the Postgraduate society?

 

While you are going through the Promised hell Down-the-road and Patiently hoping for your last Degree, why not join the Great Ormond Street Institute of Child Health (GOSICH) Postgraduate Society (PGS)? They will help you through the journey, which we all know is Pretty hard to Do, because PGS also stands for PhD Group Support.

 

The PGS was formed in 2008/09 by a few enthusiastic students – Pascal Odent, Kirsty Little, and Suzanne Bartington. It was set up because students felt isolated from each other within GOSICH and wanted a social club that would allow them to come together to share academic and social interests. Since then, the Society has been very successful, offering events such as academic talks, pub quizzes, BBQs, a film club, ice skating at Somerset House, and a Mindfulness Workshop.

Our events help you form friendships, find long-term collaborations, and get advice (research-related or otherwise) to make the rocky road during your PhD smoother and more enjoyable. This will improve your work-life balance and support your mental health, which is needed as a recent study estimated that 32% of PhD students experience depression – much higher than the prevalence in the general population (Levecque et al., 2017).

We have just created a monthly Writing Club to encourage goal setting and productivity, starting on the 5th of April from 1-3pm.  Also upcoming, we will have a summer picnic in the park with lots of free fresh food and drinks for students to socialise, connect, and enjoy time away from their usual office work.

Students are encouraged to suggest and organise event ideas, so get in touch by Facebook or Instagram (or any other method) if this article has inspired you. We are happy to bring in speakers from outside UCL or would love to hear about our own students’ work, so bring along a presentation to practice your speaking skills. Previously, we have organised successful events with a GOSICH early career researcher group, including a student networking event and a recent book presentation by Mary McClarey on how her nursing and research skills helped her to write a successful novel.

We know that the journey of a PhD can be challenging and it is therefore very important to us that students feel connected and informed at ICH. Please get in contact if you have any questions during your time here at ICH. Come forward if you have an idea about a new educational or social event or if you would like to meet new people.

Most of all, remember that PhD also stands for Passionate, hard-working, Dedication. Keep up the good work!

You can follow the GOSICH Postgraduate society on Facebook, Instagram, and Twitter:

Reference: Levecque, K., Anseel, F., De Beuckelaer, A., Van der Heyden, J., & Gisle, L. (2017). Work organization and mental health problems in PhD students. Research Policy46(4), 868-879.

Talking science: my experience of speaking at TEDx

Emma J Butcher28 January 2019

Written by Laura Katus, PhD student and soon to be post-doc at UCL Great Ormond Street Institute of Child Health. In my free time I enjoy making music and colour-coding things . Tweeting @Laura_Katus.

A few months ago, an email popped up in my inbox, containing an invitation to give a TEDx talk. I quickly scanned it, the cursor of my mouse hovering over the ‘delete’ button, convinced that this could only be spam. However, reading more closely, I remembered meeting one of the organisers a few months earlier and chatting to her about my research.

As I’m sure is true for many scientists, I liked the idea of having done a TED talk in the past. However, in this fantasy TED talk world, all the painstaking and nerve-wrecking preparation had already happened. Plus, my future self would already be a well-established researcher with loads to say, rather than a student in the middle of thesis writing.

Ultimately, the offer turned out too tempting to resist, and I agreed to give the talk. As the weeks went by, my anxiety levels rose. The process of preparation was fortunately well-guided. The organisers checked in regularly and provided encouragements and guidance on the talk outline. Despite these useful nudges, it wasn’t until arriving at the venue on the event morning and seeing a big red carpet dot that it sank in that this was happening.

When my slot came up, I was glad I had decided to start out by talking about the topic that I most enjoy: the human brain. In the rest of my talk, I explained how I had come to do (and love!) my PhD research (to find out what I do, watch the talk: https://www.youtube.com/watch?v=JkHY63rD_nc)

Reflecting back on the experience, I am extremely grateful to have had the opportunity to participate in TEDx. It was great to see speakers from all disciplines and chat to a receptive and lovely audience. Personally, the talk preparation provided just the right level of distraction from thesis writing, and it was encouraging to see other people appreciate the value in my research.

Making the most out of your PhD by combining it with travelling

Emma J Butcher14 January 2019

Written by Leevi Kerkelä, PhD student in Developmental Imaging and Biophysics Section at UCL’s Great Ormond Street Institute of Child Health, and an outdoors enthusiast

Check out the Champalimaud’s Neuroscience Programme twitter@Neuro_CF

When I moved to the UK to start my PhD project, I was eager to begin my studies in a university that prides itself on being London’s most international university. Having done my MSc in a department where PhD students were expected to visit an overseas lab to conduct part of their research, I was interested in gaining some experience abroad. At UCL, networking with international peers during conferences is common, but visiting labs overseas for actual research is rare. Students are free to go assuming they can do relevant work and get their supervisor’s approval. I spent four months of the second year of my PhD abroad and would like to share my experience to encourage others to do so.

I came up with the idea of visiting a lab abroad on a cold and rainy afternoon in Cornwall. I had spent a week surfing just to have to leave the ocean the very day I started to feel comfortable in it. The previously elusive bottom turn had started to feel natural, and I was not happy having to travel back to landlocked London. Dreaming about being able to surf on a daily basis, I searched for relevant research groups in Portugal. I was delighted to find a group in Lisbon working on MRI methods that perfectly matched the scope of my PhD project. After receiving an approval from my supervisor, I approached the principal investigator in Lisbon via e-mail. After a few e-mails and a Skype call, we agreed that I would visit the Champalimaud Centre for the Unknown for four months to work on double diffusion encoding methods for quantifying brain tissue microstructure with MRI.

Portugal has been blessed with over a thousand miles of truly magnificent coastline. This surfing gem of Ribeira d’Ilhas in Ericeira is less than an hour away from central Lisbon

During the first week of my placement, I was absolutely blown away by the beauty of my new temporary home and the quality of the research at Champalimaud. The powerful equipment allowed me to perform interesting experiments that would not have been possible at GOSH. This freedom with experimenting led me to develop a deeper understanding of MRI which has greatly helped me to make progress with my PhD project. Combining the stimulating work environment with living at the beach and enjoying the fantastic weather made these four months an unforgettable experience.

A motivated student on my first day. The Champalimaud building is an architectural masterpiece that attracts visitors for its design. Most working spaces overlook this garden in which researchers can have a relaxing break under the palm trees.

For anyone interested in visiting a research group overseas, I would give the following advice.

1) Find a research group that is relevant to your PhD project. Three or four years is a short time for finishing a PhD project, so it is crucial that your time abroad is not wasted.

2) Decide whether to briefly visit in order to learn something new or to visit for a longer period of time to conduct a short research project.

3) Speak to your supervisor and the foreign PI only after you have a good idea of what you would like to achieve with the visit.

Post-graduate studies can be a period of time filled with exceptional individual responsibility and freedom, so I strongly recommend making the most out of this time of your life.

Postscript from Faculty Graduate Tutor (Research): note that any student can also apply to take a funded research period in the USA and Canada through the UCL Bogue Fellowship Scheme.

Ups and downs: getting the upgrade report done

Emma J Butcher14 December 2018

By guest blogger Carlos A. Valencia-Hernández (@cavalenc). A 3rd year PhD student in epidemiology of ageing and cardiovascular disease (Whitehall II study, Department of Epidemiology and Public Health). He is an advocate for urban cycling and a music lover wandering around London looking for vinyl records.

So here you are. Trying to pass the upgrade from MPhil to PhD. But first of all, what is it? According to UCL guidelines, the upgrade is the process through which “the student’s progress and ability to complete their PhD” are assessed. It includes giving a presentation, having a viva, and submitting a written report. This blog entry will only focus on the upgrade report.

In this report, you must write about all your work and plans for your PhD thus far.  In other words, this is the first organised writing experience of your PhD. You started your journey some months ago. It is time to show everyone your amazing review, future plans, and perhaps some statistical analysis results. You are proud of your accomplishments and want to share them with everyone! But there are some barriers in the way and overcoming these can be frustrating. There is no magical formula and, whilst there are outliers for whom the process flows naturally, for others it can take more time. Do not compare yourself to others, or you will despair. Here are a few do’s and don’ts.

 

You cannot be 100% productive 100% of the time. Find your golden hour!

 This applies not only to the upgrade report, but to the whole thesis and other processes. Each person has their own times when they are most productive. There are early risers and night owls. Or perhaps just specific times when you are least likely to be disturbed. Identify the best hours for you and make the most of them.

 

Set a realistic time scale

You are a responsible, committed, and detail-oriented person, as well as a keen researcher. We all know it and it explains why you were admitted to a PhD. Despite this, meeting your writing deadlines can be challenging. Try to break the upgrade report into specific parts and calculate how much time you need to complete them. Include additional time for unexpected events.

 

Fast but not furious

 All (or most) of the knowledge is already in your mind. You have done the review and run the statistical models, so if you just write non-stop, what could go wrong?

Well, many things. Quantity does not always equal quality. Conveying a scientific message is challenging. You have been familiarising yourself with the topic of your PhD and the jargon related to it for months. This might not be the case for everyone who reads your upgrade report, including your supervisors, proofreaders and examiners. Take one idea at a time and develop it.

 

From failure to failure without losing enthusiasm

 Writing the upgrade report is a lengthy process with no immediate positive feedback. You can be so excited about all your ideas in the draft report sent to your supervisor(s) for comments. Then, after some hours or days, your supervisor(s) returns a sea of text highlighted with radioactive yellow or glowing cyan track-changes. All the negative thoughts about your writing skills and other abilities sweep into your brain. Keep calm. Even the best scientific writers need to be critiqued. Your supervisor(s) are helping you to make the upgrade report clearer and more understandable. They have been doing this process for quite a while. Trust them!

 

Keep the momentum: find a writing partner or look for writing retreats

 Your surroundings affect what you do and how you do it. Finding a writing partner who encourages you to keep writing is a good idea. Also, departments across UCL regularly organise writing retreats that you can attend. Peer pressure can be useful sometimes, as can the availability of a quiet environment where you can focus on quality writing.

 

Check the consistency of your document

Upgrade reports are written over the course of weeks and months. In an ideal situation, the report would be written from the introduction to the conclusion in a logical and sequential way. Real life can vary though. After finishing the first draft, you may find a newly published piece of evidence to include in the discussion, or run additional statistical tests for your results. This could mean you have other sections or sentences that are no longer relevant. Keep an eye out for this.

 

More isn’t always better

 You have worked hard on the upgrade report and may think that adding extra figures and tables would demonstrate all your time and effort. Not necessarily. Redundant tables or unclear figures could mislead the readers and suggest poor knowledge of your topic. Plus you are wasting precious space.

 

Extra help

 There is an overwhelming quantity of resources out there. You could start with UCL student psychological services, who have tips on how to get writing done.

Also try Hugh Kearns’ website and The thesis whisperer. Both have good inputs on the PhD writing process.

Bringing Cystic Fibrosis research back to the patients

Emma J Butcher29 November 2018

Written by Afroditi Avgerinou, 3rd year PhD student in the Francis Crick Institute/Institute of Child Health.

In September 2018, for the 3rd year in a row, the UK Cystic Fibrosis (CF) Trust organised the “CF’s got talent!” competition. This involved 5 young CF researchers presenting their work in layman’s terms to improve engagement with patients. I have been working on my PhD project, which is funded by the CF Trust, for 2 years and I was one of the five researchers that presented in the 2018 competition.

When I found out I had been selected to present in front of a few hundred people in a lecture theatre, and possibly thousands more online, I was terrified! At the same time, I felt honoured and a deep sense of responsibility. I did not want to let down people affected by CF, as they are putting their hope in researchers such as myself to deliver a cure. I also did not want to disappoint my supervisors or family and friends, who have been supporting me throughout my PhD.

For this reason, and because I had never delivered a public engagement talk before, I spent a whole month creating a presentation and perfecting my speech. Thankfully, the CF Trust arranged for me to share my ideas with a person with CF, who would tell me whether I had managed to get rid of the science jargon. During our two talks, she offered great help and feedback that allowed me to produce a presentation we were both satisfied with.

On the day of the presentation, my nerves returned. Even though my voice was a bit shaky, I was able to carry on and not forget my words, thanks to the number of times I had practised my talk.

During my presentation, I explained how in CF a mistake/mutation in the CFTR gene causes problems in the lung. For my project, I hope to show that the lung cells with the genetic mistake can become the solution and offer a cure for CF. To do this, I am using ex vivo gene therapy, which means gene therapy that happens outside the body. The first step of this approach is to take some of the diseased lung cells from the CF patient through nasal brushing. After this, the cells are kept in the lab and allowed to multiply. Next, a correction mechanism, called CRISPR/Cas9, is inserted into the cells, to correct the mistake in the CFTR gene. The corrected cells undergo quality control to check if they are safe and finally returned to the patient’s own lung where they will function as healthy cells and treat CF.

I felt I was successful in explaining my project to everyone in the lecture theatre. Later, I found out that many people had left very positive and kind comments on the Facebook live stream of my presentation. People watching from home also had the opportunity to vote for their favourite presentation. To my surprise, when the time came to announce the winner, my name was called. I was excited and very pleased with the result! The prize was an all-expenses paid trip to the North American Cystic Fibrosis Conference (NACFC) 2019 in Nashville. There, I will communicate the results of my work to a wide audience.

Winning the competition gave recognition to my work and all my team’s efforts. I am thankful to the CF community for voting for me, but irrespective of the win, the whole experience was very rewarding. Working in the lab, it is easy to get lost in the experiments and science, forgetting the reason why you are doing them. Being able to connect with the people that benefit from your research is inspiring and helps you refocus when things get difficult. In return, by communicating your research to patients, you are giving them hope and a promise: that you will do your best to help them and their families live a life unlimited by CF.

The full facebook stream of the event is shown below:

Original link: https://www.facebook.com/cftrust/videos/532549270526241/

Making science better: openness, reproducibility and teamwork

Emma J Butcher14 November 2018

Written by Sophie Adler-Wagstyl @sophieadler, MBPhD student and part-time post-doctoral researcher. Sophie did her PhD in the Developmental Neurosciences programme on neuroimaging of paediatric epilepsy. In her spare time she enjoys cycling and supporting Spurs.

 

 

 

 

 

 

 

PhDs can be challenging, involving tough tasks such as:

  • Learning new methods from scratch
  • Focusing only on one project and not being involved in small side projects
  • Not being part of a team and feeling lonely
  • Not knowing how to do something and being afraid to ask
  • Being asked to review a paper and not knowing how
  • Not being asked to review a paper but wanting to learn how

To address this, I helped to organise an open-science, reproducibility and teamwork session at Great Ormond Street Institute of Child Health (GOSICH) in October 2018. PhD students and post-docs spanning the breadth of research at GOSICH came along to listen and learn. Despite the diversity of methods and areas of research that people focus on at GOSICH, we discussed that there are a lot of skills required for research that are common to all of us. Many of us:

  • Have to learn stats and learn to code some of our analysis whether that be in R, Matlab, Python etc.
  • Have to think about ethics, IRAS applications, HRA approval, the GOS-ICH R&D department
  • Are doing longitudinal analyses
  • Are peer-reviewing work for the first time

And there are many more areas of mutual overlap…

In the October session, we discussed many of these topics. The outcomes of these discussions are outlined below, grouped into the areas of: collaboration and teamwork, reproducible research, open-science and peer review.

Collaboration & Teamwork

Collaboration and teamwork can help address some of the problems that PhD students face, such as learning new methods from scratch, not feeling part of a team and not being involved in side projects. However:

  • How can we create a collaborative and supportive environment where we can ask others for help?
  • How can we make our research more efficient by not repeating what others have already worked on?
  • How can we find potential collaborators?

To help with the challenges above, we have created a GOSICH SLACK workspace. This is an online space where members can post questions, events etc. and anyone from the community can respond. As well as a general channel, we have channels (groups) for early career researchers, a PREreview journal club, and social events. However, you can create a channel for anything, including for particular projects/topics, where you invite only your collaborators, a lab group, the post-doc society. If you are a current GOSICH PhD student or post-doc and would like to join the SLACK workspace, please email sophie.adler.13@ucl.ac.uk for more information.

Reproducible Research

We all want to do robust, reproducible, replicable and generalizable research. We want to know that our findings are real. We want the work to go beyond the lifespan of one PhD student or post-doc position and impact the wider scientific community.

So firstly, what is the difference between reproducible, robust, replicable and generalizable research?

@kirstie_j has a handy figure to explain it! Feel free to replace the word ‘code’ to ‘method’.

If you test a hypothesis using the same method and same data as some-one else (including your previous work), and you get the same result, your research is reproducible.

If you test the same hypothesis with a different method on the same data and get the same result, the finding is robust.

If you test the same hypothesis and use the same method on new data and get the same results, your findings are replicable.

Lastly, if you test the same hypothesis with a different method and different data, your results are generalizable.

Open-science

We can use open-science techniques to facilitate reproducible, robust, replicable and generalizable research.

 “Open Science is the practice of science in such a way that others can collaborate and contribute, where research data, lab notes and other research processes are freely available, under terms that enable reuse, redistribution and reproduction of the research and its underlying data and methods.” (fosteropenscience.eu)

Open-science practices include:

  • Publishing your work in open-access journals (so that anyone can read your work)
  • Sharing your methods (e.g. publishing them on protocols.io)
  • Sharing your data
  • Sharing your code (e.g. github.com)

 

We talked about how daunting it can be to release protocols or code but how beneficial it can be to both the wider scientific community and yourself.

PREreview

The last issue raised was about learning how to critically appraise work. One way to get practice at reviewing work in a safe and supported environment is by creating a PREreview journal club. This is a journal club that discusses and reviews preprints (manuscripts released by authors prior to peer-review).

PREreview (Post, Read, and Engage with preprint reviews) is a website hosting reviews of preprints created in journal clubs (https://www.authorea.com/inst/14743-prereview).

“Reviewing preprints benefits the authors, as they receive early feedback on their manuscript. Early-career researchers benefit from the opportunity to develop their critical thinking and peer-review skills. And the whole scientific community benefits from access to scientists’ discussions about the latest discoveries.” (https://elifesciences.org/labs/57d6b284/prereview-a-new-resource-for-the-collaborative-review-of-preprints )

We have started a PREreview channel on the GOS-ICH slack for those who are interested in improving their critical appraisal skills.

Hopefully through improving teamwork and being more open, we can help foster a supportive, collaborative environment at the Great Ormond Street Institute of Child Health. If you’re at GOSICH and want to join this endeavour – sign up to the SLACK workspace (find out how by emailing Sophie at sophie.adler.13@ucl.ac.uk) and get involved!

A pregnant PhD pause

Emma J Butcher30 October 2018

Authored by guest blogger Fran Harkness, a 3rd year student in the Medical Research Council Unit for Lifelong Health and Ageing. Studying life course predictors of psychological control, with a sudden side interest in whether controlling parenting really is that bad.

As a female PhD student I’ve had some colleagues say to me, “Now would be a great time to have a baby” and, “Think of it as an extension”.

Really? It wasn’t something I was interested in, let alone thought was possible. I’ve got training on multiple imputation that I can’t miss, chapter 4 of the thesis to finish, and an international conference coming up. But last August, two years deep into my PhD, my husband and I were eating beans on toast one Saturday morning when all our musings crystallised: Let’s have a baby!

We felt supported by my recent discovery that I’d get maternity leave. I had assumed that lowly PhD students would get nothing. More beans on toast. But in fact, many research council funded students get six months with full stipend followed by six of statutory pay. I recalled a talk by Lisa Berkman at my first UCL conference, where she discussed her finding that women offered paid maternity leave were 16% less likely to be depressed after 30 years than women without it. Financially viable and less likely to get depression. As a public health student I do like to back up my behaviour with evidence.

I was nervous about telling my supervisory panel. My PhD friends and I had already been told, “I hope you’ll still have time to write up” and, “You won’t have much time to work on your oral presentation” when relaying life events to senior colleagues. One peer caught criticism for attending her wedding instead of a conference. I hid my pregnancy through the first three months despite blocking the office toilets with vomit once and coping with daily nausea by eating an odd amount of cream crackers.

In the end it burst out during a meeting. My friend was also present and exclaimed “No! Don’t tell them” as I opened my mouth, such was our joint anxiety about me being told off. PhD students are usually full of worry when it comes to ‘things getting in the way of handing in on time’. Luckily my supervisors were extremely supportive, from their suggestions of salt and vinegar crisps for my constant sickness, to reminders to submit my leave application so I didn’t miss any stipend payments.

In the remaining months before birth, I worked extremely hard and did most of my analyses, in case I forget how to whilst away. I also sketched out a plan for outstanding work and ensured everything was triple backed up, with my password (ahem, secretly) written down. A colleague advised me that even a takeaway coffee cup with a challenging lid could cause upset on returning to work, so I didn’t want to leave any gaps to fall through. The admin involved in planning my break was surprisingly easy. All I needed was a maternity exemption form from my midwife emailed to the unit administrator, who logged the pause in my studies and advised me on baby monitors.

New co-working space

So now my baby is six weeks old. I wouldn’t exactly term this period a PhD extension. Unless research is aided by writing up complex associations on three hours sleep with breast milk dripping onto the keyboard. Plus, I like busying myself by staring lovingly at my baby, rather than tackling the writing. I’ll be off for six months doing that, and when I return, my husband will use the remainder for shared parental leave.

I am a bit apprehensive about going back. I can’t decide whether my thesis dedication will read, ‘Darling Robin, thanks for wangling me a six month breather’, or, ‘Dear Robin, thanks for seriously setting me back’. But as I write one-handed with him sleeping on my chest and my nose buried in his gorgeous smell, I just feel very happy we were able to have him.

The three minute thesis (3MT) – a mountain drag-lift for PhD students

Emma J Butcher18 October 2018

Written by Jonathan Lambert

For most research students, including myself, writing a PhD thesis feels like trudging up a seemingly endless mountain. It is a lonely experience made more difficult because only three or four people may ever read our careful efforts. But I want to encourage you. Just imagine, for a moment, packaging up all your hard work into a three minute spoken presentation that conveys the big picture of your thesis to a potentially world-wide audience. The presentation would identify the value of your research in potentially improving human health and wellbeing, communicate your passion for the subject, and highlight the wider impact of your findings to society. Imagine how helpful that talk would be when meeting potential employers or completing grant applications, not to mention helping construct the final thesis. Then of course there is the buzz of using your presentation to share your work with family and friends in a way that is accessible to all. This could be the perfect opportunity to get excited about your work and help you feel like you’ve just found a lift to help you up the mountain.

Well, this is precisely the concept of the three minute thesis (3MT), developed by The University of Queensland, Australia, in 2008. The competition has grown in popularity and spread internationally to over 600 universities, including UCL. The Great Ormond Street Institute of Child Health (GOSICH), UCL, held their first 3MT competition in 2016, at which I presented my project entitled “Less is More: the efficacy of gene therapy to treat Fabry Disease”. The slide developed to help communicate my thesis is shown below.

 

 

In my 3MT presentation, I discussed my research on Fabry disease, a genetic metabolic disorder primarily affecting the heart, brain and kidneys. The disease is caused by an enzyme deficiency in lysosomes, which are compartments within cells. Lysosomes may be conceptualised as a “wheelie bin”. I asked the audience to imagine the situation if a local waste removal company went permanently on strike: waste would accumulate in bins resulting in anxiety, illness and death to the local residents. On a cellular level, this situation is similar to Fabry disease. The enzyme deficiency, which results from specific gene mutations, leads to accumulation of waste in lysosomes and ultimately cell death. My research investigated whether gene therapy, which involves inserting a correct gene copy into patient cells using a virus vector, may be a good treatment.

I found that gene therapy produced a dose-dependent increase in enzyme activity in target cells. A low dose produced an enzyme equally efficient at breaking down waste as in healthy cells, but a high dose produced a significantly less efficient enzyme. In the talk, I put these results into the context of the waste removal company to help the audience appreciate the relevance of these findings; a low dose gene therapy may be thought of as a single workman, focused on his job and efficient at clearing waste from bins. A high dose delivery is like a team of workmen, distracted by arguing and talking with each other so that they can’t work efficiently. In other words, a lower dose of gene therapy may treat patients more efficiently than a high dose – “less may be more”. I concluded my talk with discussion of my on-going work, studying the potential of gene therapy to repair damage to the mitochondria, the “power supply” of the cell. The potential impact of this was highlighted by explaining that, if gene therapy could repair mitochondrial damage, this may be equivalent to giving back “cellular mojo” to enable cells to repair and save the lives of Fabry disease patients.

My presentation won the 2016 UCL Final and came runner-up in the 2016 Vitae 3MT UK National Final, held as part of the annual Vitae Career Researchers international conference. Participation in the 3MT competition not only improved my presentation and communication skills but inspired me in public engagement, teaching activities, and a successful grant application to the National Institute of Health Research (NIHR) Biomedical Research Centre at GOSICH that funded the final phase of my project.

So when you are next knee deep in PhD mountain snow, struggling to write your thesis, don’t panic. Get a clean sheet of paper, a cup of tea, and create a story-board of your project. Sign up for the next 3MT competition and get involved with public engagement activities. Like a mountain drag-lift, this process will help you to complete the climb and finish your thesis.