Ups and downs: getting the upgrade report done

By Emma J Butcher, on 14 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

By Emma J Butcher, on 29 November 2018

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

In September 2018, for the 3^rd 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

By Emma J Butcher, on 14 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

By Emma J Butcher, on 30 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

By Emma J Butcher, on 18 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.

Finished is better than perfect!

By Emma J Butcher, on 23 August 2018

Authored by Victoria Garfield, a postdoctoral researcher in genetic epidemiology (UCL Institute of Cardiovascular Science). Victoria did her PhD in the Department of Behavioural Science & Health and her current research involves using genetic and epidemiological methods to understand the relationship between diabetes and the brain. In her spare time, she likes to swim and work her way around London (and the world!) eating delicious food.  

“A PhD is a bunch of projects that you work on for a few years and then you write them up in one big document.” Truth. That’s what that quote is, the truth. It was said by a good friend of mine with a PhD. A PhD is a collection of related projects that you work on for a few years (usually three to four in the UK), then write up in what is essentially, a book. However, to get to that point, one must endure…drumroll… THE FINAL YEAR. Yikes. I remember in my first and second year, I was completely in awe of final-year PhD students, not to mention the new postdocs. How had they done it?!

Well, the final year is a wee bit different for each of us. Some of the major factors are:

• How much analysis or data collection is left;
• How much of your upgrade report you can use in the final thesis;
• Availability of your supervisor(s) (who are generally extremely busy);
• When funding ends (and thus, when you’ll need a job so you don’t starve);
• And crucially, your personal life, including both mental and physical health.

My final year was an overall positive experience, but naturally, I felt overwhelmed at times. I know I’m not alone here, as friends with PhDs confirm having similar feelings. Some of the most important things on your final year to-do list are:

• Knowing when you’ve done enough data collection and/or analysis to discuss starting to write with your supervisor(s);
• Having clear timelines for sending chapters to your supervisor(s) (if they agreed to read these before a full draft);
• Establishing with your supervisor(s) who will read which chapters;
• Deciding when you will send a full draft to your supervisor(s) (exact date);
• Choosing good examiners with plenty of time before the planned viva;
• Agreeing your submission date with your supervisor(s);
• Knowing when your supervisor(s) are away.

I turned 30 in my final year, which is obviously a big deal, so naturally, I celebrated my birthday with my family on HOLIDAY in Spain – yep, that’s right, in my final year!

A VERY important point that deserves its own paragraph is that you MUST plan a break for yourself (no, you do NOT have to spend 24/7 writing and obsessing). We all need breaks. I took a few holidays in my final year and…I STILL GOT MY PHD ON TIME! Given that all PhD students love research, let’s not forget that evidence shows that time away from work (I mean really taking time off, without checking emails), means we feel refreshed and are more productive when we return.

Me admiring the amazingness that is Northern Norway (just outside of Tromsø) – also in my final year.

Now, I want to briefly come back to the other most important points. Knowing when to stop analysis is often a difficult one. For me, this happened via a Skype call with my supervisor when we almost organically both said, “that’s probably enough analyses now, time to focus on writing”. At this point, I had four studies to write up into results chapters, two of which were quite substantial and two slightly smaller. I emailed my other supervisors to let them know and everyone agreed that I had plenty of work for the thesis. This was in May and my funding was until the end of December, so plenty of time to focus on writing. I had some of my thesis written up already, but did the bulk of writing between June and late September, when I sent a full draft to my supervisors. Then, as I started working full-time as a (impostor!) postdoc, it took a little longer than I wanted to make amendments before sending my supervisors another draft then preparing for submission.

My fiancée and I in Norway – on holiday (no email or thesis!) in my final year (you get the point now, right?!)

Another crucial point for me was choosing examiners. I did this with plenty of time before the viva – so had lots of time to complete the paperwork and wait for central UCL to confirm that they approved the examiner choice (which usually takes a few weeks). This then leads me swiftly to…another drumroll…THE VIVA. The viva is a rather surreal experience in mine and others’ opinions. My viva was incredibly positive, but also long (four hours) and I only realised about a week after how exhausted I was. So, I obviously then took two days off to be a couch potato and order pizza in the middle of the day. My examiners were very positive about my thesis and wanted to discuss it at length. It was a professional but friendly atmosphere and I was appreciative that two esteemed academics had taken the time to read my research in depth. I passed with minor corrections (you get three months to do these) and although it can feel difficult to go back to your thesis and do the corrections, you know then that you have done it. YOU HAVE PRETTY MUCH GOT YOUR PHD. Now, go and celebrate, AGAIN (you will celebrate as soon as you finish your viva, obviously). My final recommendation is to have a mock viva – I had one with one of my PhD mentors (a mid-career researcher) and the head of our group, which I found invaluable.

Viva present I got from two amazing UCL friends – although you may not get a Garfield toy that says Dr Garfield on his badge (unless your surname is also Garfield), at least one person you know will get you something that says ‘Dr’ on it, so get that #PhDone!